I: pbuilder: network access will be disabled during build
I: Current time: Mon Apr 20 06:23:12 +14 2026
I: pbuilder-time-stamp: 1776615792
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [rdkit_202409.6-2.dsc]
I: copying [./rdkit_202409.6.orig.tar.xz]
I: copying [./rdkit_202409.6-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./rdkit_202409.6-2.dsc: unsupported subcommand
dpkg-source: info: extracting rdkit in rdkit-202409.6
dpkg-source: info: unpacking rdkit_202409.6.orig.tar.xz
dpkg-source: info: unpacking rdkit_202409.6-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying NoDownloads.patch
dpkg-source: info: applying postgres_Makefile_fixes.patch
dpkg-source: info: applying sphinx_imgconverter.patch
dpkg-source: info: applying postgres_alternative_test_outputs.patch
dpkg-source: info: applying sphinx_compile_fixes.patch
dpkg-source: info: applying extra_float_digits
dpkg-source: info: applying postgres_cmakelists_fixes.patch
dpkg-source: info: applying disable_pgsql_test.patch
dpkg-source: info: applying fix_inchi_linking.patch
dpkg-source: info: applying disable_inchi_test.patch
dpkg-source: info: applying disable_python_test.patch
dpkg-source: info: applying disable_riscv64_timeout_tests.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3364963/tmp/hooks/D01_modify_environment starting
debug: Running on ionos15-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Apr 19 16:23 /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/3364963/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/3364963/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DIRSTACK=()
DISTRIBUTION=trixie
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=1d708fc1cfb74b58b0f766d3f6828a6b
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=3364963
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.0dUPBDtL/pbuilderrc_iJ7j --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0dUPBDtL/b2 --logfile b2/build.log rdkit_202409.6-2.dsc'
SUDO_GID=111
SUDO_UID=106
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3364963/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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: architecture-is-64-bit, architecture-is-little-endian, bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-numpy-dev, libboost-program-options-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo2-dev, libcoordgen-dev, libeigen3-dev, libfreetype-dev, libinchi-dev (>= 1.07.1+dfsg-2), libmaeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-myst-parser, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-pytest, python3-recommonmark, python3-sphinx, python3-sqlalchemy, rapidjson-dev, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19803 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 architecture-is-64-bit; however:
Package architecture-is-64-bit is not installed.
pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however:
Package architecture-is-little-endian is not installed.
pbuilder-satisfydepends-dummy depends on bison; however:
Package bison is not installed.
pbuilder-satisfydepends-dummy depends on catch2; however:
Package catch2 is not installed.
pbuilder-satisfydepends-dummy depends on cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on doxygen; however:
Package doxygen is not installed.
pbuilder-satisfydepends-dummy depends on flex; however:
Package flex is not installed.
pbuilder-satisfydepends-dummy depends on imagemagick; however:
Package imagemagick is not installed.
pbuilder-satisfydepends-dummy depends on latexmk; however:
Package latexmk is not installed.
pbuilder-satisfydepends-dummy depends on libboost-dev; however:
Package libboost-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however:
Package libboost-iostreams-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-numpy-dev; however:
Package libboost-numpy-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however:
Package libboost-program-options-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-python-dev; however:
Package libboost-python-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however:
Package libboost-regex-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-system-dev; however:
Package libboost-system-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however:
Package libboost-thread-dev is not installed.
pbuilder-satisfydepends-dummy depends on libcairo2-dev; however:
Package libcairo2-dev is not installed.
pbuilder-satisfydepends-dummy depends on libcoordgen-dev; however:
Package libcoordgen-dev is not installed.
pbuilder-satisfydepends-dummy depends on libeigen3-dev; however:
Package libeigen3-dev is not installed.
pbuilder-satisfydepends-dummy depends on libfreetype-dev; however:
Package libfreetype-dev is not installed.
pbuilder-satisfydepends-dummy depends on libinchi-dev (>= 1.07.1+dfsg-2); however:
Package libinchi-dev is not installed.
pbuilder-satisfydepends-dummy depends on libmaeparser-dev; however:
Package libmaeparser-dev is not installed.
pbuilder-satisfydepends-dummy depends on librsvg2-bin; however:
Package librsvg2-bin is not installed.
pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however:
Package libsqlite3-dev is not installed.
pbuilder-satisfydepends-dummy depends on pandoc; however:
Package pandoc is not installed.
pbuilder-satisfydepends-dummy depends on postgresql-server-dev-all; however:
Package postgresql-server-dev-all is not installed.
pbuilder-satisfydepends-dummy depends on python3-dev; however:
Package python3-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-myst-parser; however:
Package python3-myst-parser is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
pbuilder-satisfydepends-dummy depends on python3-pandas; however:
Package python3-pandas is not installed.
pbuilder-satisfydepends-dummy depends on python3-pil | python3-imaging; however:
Package python3-pil is not installed.
Package python3-imaging is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest; however:
Package python3-pytest is not installed.
pbuilder-satisfydepends-dummy depends on python3-recommonmark; however:
Package python3-recommonmark is not installed.
pbuilder-satisfydepends-dummy depends on python3-sphinx; however:
Package python3-sphinx is not installed.
pbuilder-satisfydepends-dummy depends on python3-sqlalchemy; however:
Package python3-sqlalchemy is not installed.
pbuilder-satisfydepends-dummy depends on rapidjson-dev; however:
Package rapidjson-dev is not installed.
pbuilder-satisfydepends-dummy depends on tex-gyre; however:
Package tex-gyre is not installed.
pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however:
Package texlive-fonts-recommended is not installed.
pbuilder-satisfydepends-dummy depends on texlive-latex-base; however:
Package texlive-latex-base is not installed.
pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however:
Package texlive-latex-extra is not installed.
pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however:
Package texlive-latex-recommended is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bison{a} bsdextrautils{a} ca-certificates{a} catch2{a} clang-19{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} girepository-tools{a} groff-base{a} hicolor-icon-theme{a} icu-devtools{a} imagemagick{a} imagemagick-7-common{a} imagemagick-7.q16{a} intltool-debian{a} latexmk{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libblkid-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcatch2-dev{a} libclang-common-19-dev{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcoordgen-dev{a} libcoordgen3{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libffi8{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} libgnutls30t64{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} libicu76{a} libidn2-0{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} libldap2{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} libnghttp3-9{a} libnuma1{a} libobjc-14-dev{a} libobjc4{a} libopenjp2-7{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{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} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{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} libtasn1-6{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{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-common-dev{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-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-iniconfig{a} python3-jinja2{a} python3-markdown-it{a} python3-markupsafe{a} python3-mdit-py-plugins{a} python3-mdurl{a} python3-minimal{a} python3-myst-parser{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pluggy{a} python3-pygments{a} python3-pytest{a} python3-pytz{a} python3-recommonmark{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sqlalchemy{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-yaml{a} python3.13{a} python3.13-dev{a} python3.13-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 papers 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, 370 newly installed, 0 to remove and 0 not upgraded.
Need to get 429 MB of archives. After unpacking 2168 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 flex amd64 2.6.4-8.2+b4 [423 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.1 [318 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.1 [391 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.19.7-1 [11.7 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b3 [189 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.19.7-1 [15.3 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.19.7-1 [520 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.0-2 [1513 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 liblqr-1-0 amd64 0.4.2-2.1+b2 [29.5 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.5.4-4 [416 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 libraw23t64 amd64 0.21.3-1+b1 [390 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [67.4 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 libmagickcore-7.q16-10 amd64 8:7.1.1.43+dfsg1-1 [1843 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 libmagickwand-7.q16-10 amd64 8:7.1.1.43+dfsg1-1 [340 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 postgresql-client-common all 274 [46.5 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 postgresql-common-dev all 274 [71.8 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 ssl-cert all 1.1.3 [16.8 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get: 53 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0050 [42.7 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 postgresql-common all 274 [111 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2+b1 [138 kB]
Get: 71 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.3+ds-2+b1 [5081 kB]
Get: 75 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 83 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 86 http://deb.debian.org/debian trixie/main amd64 architecture-properties amd64 0.2.6 [2336 B]
Get: 87 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 88 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 libcatch2-dev amd64 3.7.1-0.5 [613 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 catch2 all 3.7.1-0.5 [5144 B]
Get: 94 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libclang-cpp19 amd64 1:19.1.7-1+b1 [13.2 MB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 libgc1 amd64 1:8.2.8-1 [247 kB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 libobjc4 amd64 14.2.0-17 [42.7 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 libobjc-14-dev amd64 14.2.0-17 [170 kB]
Get: 101 http://deb.debian.org/debian trixie/main amd64 libclang-common-19-dev amd64 1:19.1.7-1+b1 [740 kB]
Get: 102 http://deb.debian.org/debian trixie/main amd64 llvm-19-linker-tools amd64 1:19.1.7-1+b1 [1261 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 libclang1-19 amd64 1:19.1.7-1+b1 [7614 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 clang-19 amd64 1:19.1.7-1+b1 [116 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-1 [2268 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 109 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 111 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-1 [109 kB]
Get: 115 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 122 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 128 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-1 [12.0 MB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 137 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 140 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 141 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 142 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250308 [115 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB]
Get: 145 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 doxygen amd64 1.9.8+ds-2.1 [5017 kB]
Get: 148 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2.1 [463 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 fonts-lmodern all 2.005-1 [4540 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 native-architecture all 0.2.6 [2264 B]
Get: 151 http://deb.debian.org/debian trixie/main amd64 libgirepository-2.0-0 amd64 2.84.0-2 [141 kB]
Get: 152 http://deb.debian.org/debian trixie/main amd64 girepository-tools amd64 2.84.0-2 [148 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB]
Get: 154 http://deb.debian.org/debian trixie/main amd64 libicu76 amd64 76.1-3 [9721 kB]
Get: 155 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 76.1-3 [215 kB]
Get: 156 http://deb.debian.org/debian trixie/main amd64 imagemagick-7.q16 amd64 8:7.1.1.43+dfsg1-1 [726 kB]
Get: 157 http://deb.debian.org/debian trixie/main amd64 imagemagick amd64 8:7.1.1.43+dfsg1-1 [20.0 kB]
Get: 158 http://deb.debian.org/debian trixie/main amd64 tex-common all 6.19 [29.4 kB]
Get: 159 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB]
Get: 160 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB]
Get: 161 http://deb.debian.org/debian trixie/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5+b1 [157 kB]
Get: 162 http://deb.debian.org/debian trixie/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5+b1 [49.4 kB]
Get: 163 http://deb.debian.org/debian trixie/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5+b1 [63.0 kB]
Get: 164 http://deb.debian.org/debian trixie/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5+b1 [115 kB]
Get: 165 http://deb.debian.org/debian trixie/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get: 166 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 167 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 168 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 169 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB]
Get: 170 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB]
Get: 171 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 172 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB]
Get: 173 http://deb.debian.org/debian trixie/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB]
Get: 174 http://deb.debian.org/debian trixie/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB]
Get: 175 http://deb.debian.org/debian trixie/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB]
Get: 176 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB]
Get: 177 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB]
Get: 178 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB]
Get: 179 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB]
Get: 180 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB]
Get: 181 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB]
Get: 182 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB]
Get: 183 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB]
Get: 184 http://deb.debian.org/debian trixie/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.1 [59.0 kB]
Get: 185 http://deb.debian.org/debian trixie/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5+b1 [8504 kB]
Get: 186 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 187 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2024.20250114-1 [22.8 MB]
Get: 188 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2024.20250114-1 [1282 kB]
Get: 189 http://deb.debian.org/debian trixie/main amd64 latexmk all 1:4.86~ds-1 [507 kB]
Get: 190 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B]
Get: 191 http://deb.debian.org/debian trixie/main amd64 uuid-dev amd64 2.40.4-5 [47.8 kB]
Get: 192 http://deb.debian.org/debian trixie/main amd64 libblkid-dev amd64 2.40.4-5 [205 kB]
Get: 193 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1+b2 [10.6 MB]
Get: 194 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4.1+b2 [234 kB]
Get: 195 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4.1+b2 [236 kB]
Get: 196 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4.1+b2 [240 kB]
Get: 197 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83-dev amd64 1.83.0-4.1+b2 [246 kB]
Get: 198 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83.0 amd64 1.83.0-4.1+b2 [230 kB]
Get: 199 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.1+b2 [334 kB]
Get: 200 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.1+b2 [373 kB]
Get: 201 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83-dev amd64 1.83.0-4.1+b2 [240 kB]
Get: 202 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B]
Get: 203 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83.0 amd64 1.83.0-4.1+b2 [330 kB]
Get: 204 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 76.1-3 [10.8 MB]
Get: 205 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83-dev amd64 1.83.0-4.1+b2 [346 kB]
Get: 206 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4.1+b2 [261 kB]
Get: 207 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B]
Get: 208 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83.0 amd64 1.83.0-4.1+b2 [306 kB]
Get: 209 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83.0 amd64 1.83.0-4.1+b2 [242 kB]
Get: 210 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83-dev amd64 1.83.0-4.1+b2 [246 kB]
Get: 211 http://deb.debian.org/debian trixie/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B]
Get: 212 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.1+b2 [347 kB]
Get: 213 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4.1+b2 [376 kB]
Get: 214 http://deb.debian.org/debian trixie/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B]
Get: 215 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB]
Get: 216 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB]
Get: 217 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 218 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB]
Get: 219 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.2-2 [10.3 kB]
Get: 220 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB]
Get: 221 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 222 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 223 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 224 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.2-2 [26.1 kB]
Get: 225 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83-dev amd64 1.83.0-4.1+b2 [328 kB]
Get: 226 http://deb.debian.org/debian trixie/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B]
Get: 227 http://deb.debian.org/debian trixie/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B]
Get: 228 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83.0 amd64 1.83.0-4.1+b2 [231 kB]
Get: 229 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83-dev amd64 1.83.0-4.1+b2 [232 kB]
Get: 230 http://deb.debian.org/debian trixie/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B]
Get: 231 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1+b2 [269 kB]
Get: 232 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83-dev amd64 1.83.0-4.1+b2 [277 kB]
Get: 233 http://deb.debian.org/debian trixie/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B]
Get: 234 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB]
Get: 235 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 236 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB]
Get: 237 http://deb.debian.org/debian trixie/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB]
Get: 238 http://deb.debian.org/debian trixie/main amd64 libcairo-script-interpreter2 amd64 1.18.2-2 [58.8 kB]
Get: 239 http://deb.debian.org/debian trixie/main amd64 libpng-dev amd64 1.6.47-1.1 [366 kB]
Get: 240 http://deb.debian.org/debian trixie/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB]
Get: 241 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 242 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 243 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 244 http://deb.debian.org/debian trixie/main amd64 libfontconfig-dev amd64 2.15.0-2.1 [414 kB]
Get: 245 http://deb.debian.org/debian trixie/main amd64 libffi-dev amd64 3.4.7-1 [60.8 kB]
Get: 246 http://deb.debian.org/debian trixie/main amd64 libsepol-dev amd64 3.8-1 [372 kB]
Get: 247 http://deb.debian.org/debian trixie/main amd64 libpcre2-16-0 amd64 10.45-1 [281 kB]
Get: 248 http://deb.debian.org/debian trixie/main amd64 libpcre2-32-0 amd64 10.45-1 [268 kB]
Get: 249 http://deb.debian.org/debian trixie/main amd64 libpcre2-posix3 amd64 10.45-1 [63.5 kB]
Get: 250 http://deb.debian.org/debian trixie/main amd64 libpcre2-dev amd64 10.45-1 [853 kB]
Get: 251 http://deb.debian.org/debian trixie/main amd64 libselinux1-dev amd64 3.8-4 [169 kB]
Get: 252 http://deb.debian.org/debian trixie/main amd64 libmount-dev amd64 2.40.4-5 [29.6 kB]
Get: 253 http://deb.debian.org/debian trixie/main amd64 libsysprof-capture-4-dev amd64 48~beta-2 [48.0 kB]
Get: 254 http://deb.debian.org/debian trixie/main amd64 libgio-2.0-dev amd64 2.84.0-2 [1685 kB]
Get: 255 http://deb.debian.org/debian trixie/main amd64 libglib2.0-data all 2.84.0-2 [1286 kB]
Get: 256 http://deb.debian.org/debian trixie/main amd64 libglib2.0-bin amd64 2.84.0-2 [128 kB]
Get: 257 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 258 http://deb.debian.org/debian trixie/main amd64 libgio-2.0-dev-bin amd64 2.84.0-2 [164 kB]
Get: 259 http://deb.debian.org/debian trixie/main amd64 libglib2.0-dev-bin amd64 2.84.0-2 [52.9 kB]
Get: 260 http://deb.debian.org/debian trixie/main amd64 libglib2.0-dev amd64 2.84.0-2 [53.6 kB]
Get: 261 http://deb.debian.org/debian trixie/main amd64 libpixman-1-dev amd64 0.44.0-3 [11.4 kB]
Get: 262 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get: 263 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB]
Get: 264 http://deb.debian.org/debian trixie/main amd64 x11proto-core-dev all 2024.1-1 [3312 B]
Get: 265 http://deb.debian.org/debian trixie/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB]
Get: 266 http://deb.debian.org/debian trixie/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB]
Get: 267 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB]
Get: 268 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB]
Get: 269 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB]
Get: 270 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB]
Get: 271 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB]
Get: 272 http://deb.debian.org/debian trixie/main amd64 libxcb-render0-dev amd64 1.17.0-2+b1 [118 kB]
Get: 273 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0-dev amd64 1.17.0-2+b1 [108 kB]
Get: 274 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB]
Get: 275 http://deb.debian.org/debian trixie/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b4 [35.8 kB]
Get: 276 http://deb.debian.org/debian trixie/main amd64 libcairo2-dev amd64 1.18.2-2 [43.0 kB]
Get: 277 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 278 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 279 http://deb.debian.org/debian trixie/main amd64 libcoordgen3 amd64 3.0.2-1+b2 [225 kB]
Get: 280 http://deb.debian.org/debian trixie/main amd64 libcoordgen-dev amd64 3.0.2-1+b2 [46.9 kB]
Get: 281 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get: 282 http://deb.debian.org/debian trixie/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB]
Get: 283 http://deb.debian.org/debian trixie/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB]
Get: 284 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB]
Get: 285 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get: 286 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB]
Get: 287 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB]
Get: 288 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB]
Get: 289 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB]
Get: 290 http://deb.debian.org/debian trixie/main amd64 libinchi1.07 amd64 1.07.3+dfsg-1 [557 kB]
Get: 291 http://deb.debian.org/debian trixie/main amd64 libinchi-dev amd64 1.07.3+dfsg-1 [19.6 kB]
Get: 292 http://deb.debian.org/debian trixie/main amd64 liblua5.4-0 amd64 5.4.7-1+b2 [147 kB]
Get: 293 http://deb.debian.org/debian trixie/main amd64 libmaeparser1 amd64 1.3.1-1+b2 [94.0 kB]
Get: 294 http://deb.debian.org/debian trixie/main amd64 libmaeparser-dev amd64 1.3.1-1+b2 [13.7 kB]
Get: 295 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB]
Get: 296 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB]
Get: 297 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB]
Get: 298 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 299 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get: 300 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB]
Get: 301 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB]
Get: 302 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB]
Get: 303 http://deb.debian.org/debian trixie/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB]
Get: 304 http://deb.debian.org/debian trixie/main amd64 libpfm4 amd64 4.13.0+git83-g91970fe-1 [368 kB]
Get: 305 http://deb.debian.org/debian trixie/main amd64 libpq5 amd64 17.4-1+b1 [226 kB]
Get: 306 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB]
Get: 307 http://deb.debian.org/debian trixie/main amd64 libpq-dev amd64 17.4-1+b1 [149 kB]
Get: 308 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB]
Get: 309 http://deb.debian.org/debian trixie/main amd64 librsvg2-2 amd64 2.59.90+dfsg-2 [1794 kB]
Get: 310 http://deb.debian.org/debian trixie/main amd64 librsvg2-bin amd64 2.59.90+dfsg-2 [1962 kB]
Get: 311 http://deb.debian.org/debian trixie/main amd64 libsqlite3-dev amd64 3.46.1-2 [1107 kB]
Get: 312 http://deb.debian.org/debian trixie/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [794 kB]
Get: 313 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB]
Get: 314 http://deb.debian.org/debian trixie/main amd64 libz3-dev amd64 4.13.3-1 [107 kB]
Get: 315 http://deb.debian.org/debian trixie/main amd64 llvm-19-runtime amd64 1:19.1.7-1+b1 [551 kB]
Get: 316 http://deb.debian.org/debian trixie/main amd64 llvm-19 amd64 1:19.1.7-1+b1 [16.4 MB]
Get: 317 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 318 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB]
Get: 319 http://deb.debian.org/debian trixie/main amd64 llvm-19-tools amd64 1:19.1.7-1+b1 [511 kB]
Get: 320 http://deb.debian.org/debian trixie/main amd64 llvm-19-dev amd64 1:19.1.7-1+b1 [43.2 MB]
Get: 321 http://deb.debian.org/debian trixie/main amd64 pandoc-data all 3.1.11.1-3 [459 kB]
Get: 322 http://deb.debian.org/debian trixie/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB]
Get: 323 http://deb.debian.org/debian trixie/main amd64 postgresql-client-17 amd64 17.4-1+b1 [2038 kB]
Get: 324 http://deb.debian.org/debian trixie/main amd64 postgresql-server-dev-17 amd64 17.4-1+b1 [1318 kB]
Get: 325 http://deb.debian.org/debian trixie/main amd64 postgresql-server-dev-all all 274 [13.5 kB]
Get: 326 http://deb.debian.org/debian trixie/main amd64 preview-latex-style all 13.2-1 [350 kB]
Get: 327 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB]
Get: 328 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 329 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.17.0-1 [117 kB]
Get: 330 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get: 331 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 332 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB]
Get: 333 http://deb.debian.org/debian trixie/main amd64 python3-commonmark all 0.9.1-8 [45.5 kB]
Get: 334 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 335 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 336 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB]
Get: 337 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 338 http://deb.debian.org/debian trixie/main amd64 python3-greenlet amd64 3.1.0-1+b2 [165 kB]
Get: 339 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB]
Get: 340 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 341 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 342 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB]
Get: 343 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.5-2 [107 kB]
Get: 344 http://deb.debian.org/debian trixie/main amd64 python3-mdurl all 0.1.2-1 [9444 B]
Get: 345 http://deb.debian.org/debian trixie/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB]
Get: 346 http://deb.debian.org/debian trixie/main amd64 python3-mdit-py-plugins all 0.4.2-1 [32.4 kB]
Get: 347 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-5 [617 kB]
Get: 348 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-2 [114 kB]
Get: 349 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB]
Get: 350 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 351 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-5 [468 kB]
Get: 352 http://deb.debian.org/debian trixie/main amd64 python3-myst-parser all 4.0.1-1 [78.8 kB]
Get: 353 http://deb.debian.org/debian trixie/main amd64 python3-pytz all 2025.1-3 [150 kB]
Get: 354 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2025.1-3 [4004 B]
Get: 355 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-8+b1 [4517 kB]
Get: 356 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-8 [3097 kB]
Get: 357 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB]
Get: 358 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 359 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.4-1 [250 kB]
Get: 360 http://deb.debian.org/debian trixie/main amd64 python3-recommonmark all 0.7.1+ds-8 [17.6 kB]
Get: 361 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 362 http://deb.debian.org/debian trixie/main amd64 python3-sqlalchemy all 2.0.32+ds1-1 [1196 kB]
Get: 363 http://deb.debian.org/debian trixie/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB]
Get: 364 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 365 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB]
Get: 366 http://deb.debian.org/debian trixie/main amd64 tex-gyre all 20180621-6 [6209 kB]
Get: 367 http://deb.debian.org/debian trixie/main amd64 texlive-fonts-recommended all 2024.20250114-1 [4991 kB]
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Get: 370 http://deb.debian.org/debian trixie/main amd64 texlive-latex-extra all 2024.20250114-1 [24.7 MB]
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Building format(s) --all.
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-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/3364963/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/3364963/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/rdkit-202409.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202409.6-2_source.changes
dpkg-buildpackage: info: source package rdkit
dpkg-buildpackage: info: source version 202409.6-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael Banck <mbanck@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
pg_buildext checkcontrol
dh clean --with python3 --buildsystem=cmake
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6'
find /build/reproducible-path/rdkit-202409.6 -name "*.pyc" | xargs rm -f
rm -f -r Projects/DbCLI/testData/bzr/ rdkit/Chem/inchi.py
rm -f -r Docs/Book/_build Code/docs rdkit/docs Code/doxygen_sqlite3.db
rm -f \
Code/ForceField/MMFF/test_data/MMFF94_dative_min.sdf \
Code/ForceField/MMFF/test_data/MMFF94_dative_min_from_SMILES.sdf \
Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min.sdf \
Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min_from_SMILES.sdf \
Code/ForceField/MMFF/test_data/MMFF94_reference.log \
Code/ForceField/MMFF/test_data/MMFF94s_reference.log \
Code/ForceField/MMFF/test_data/testMMFFForceField.log \
Code/GraphMol/Depictor/test_data/cis_trans_cpp.out.sdf \
Code/GraphMol/Depictor/test_data/collisions.out.sdf \
Code/GraphMol/Depictor/test_data/first_200.out.sdf \
Code/GraphMol/Depictor/test_data/test1.out.sdf \
Code/GraphMol/FileParsers/test_data/blah.sdf \
Code/GraphMol/FileParsers/test_data/cdk2_stereo.sdf \
Code/GraphMol/FileParsers/test_data/outNCI_few.sdf \
Code/GraphMol/FileParsers/test_data/outNCI_few.tdt \
Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf \
Code/GraphMol/FileParsers/test_data/outSmiles.csv \
Code/GraphMol/ForceFieldHelpers/UFF/test_data/Issue62.sdf \
Code/GraphMol/MolAlign/test_data/ref_e2_pyCrippenO3A.sdf \
Code/GraphMol/SLNParse/lex.yysln.cpp \
Code/GraphMol/SLNParse/sln.tab.cpp \
Code/GraphMol/SLNParse/sln.tab.hpp \
Code/GraphMol/SmilesParse/lex.yysmarts.cpp \
Code/GraphMol/SmilesParse/lex.yysmiles.cpp \
Code/GraphMol/SmilesParse/smarts.tab.cpp \
Code/GraphMol/SmilesParse/smarts.tab.hpp \
Code/GraphMol/SmilesParse/smiles.tab.cpp \
Code/GraphMol/SmilesParse/smiles.tab.hpp \
Code/GraphMol/Wrap/test_data/outNCI_few.sdf \
Code/GraphMol/Wrap/test_data/outSmiles.txt \
Code/RDGeneral/versions.cpp \
Docs/Book/Cartridge.rst \
Docs/Book/Install.rst \
Docs/Book/Overview.rst \
rdkit/ML/Data/test_data/testgeneral.dat.pkl \
rdkit/ML/Data/test_data/testquant.qdat.pkl
rm -f Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps
dh_auto_clean
rm -f -rf /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-*
make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6'
dh_autoreconf_clean -O--buildsystem=cmake
dh_clean -O--buildsystem=cmake
debian/rules binary
dh binary --with python3 --buildsystem=cmake
dh_update_autotools_config -O--buildsystem=cmake
dh_autoreconf -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6'
dh_auto_configure -- -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DRDK_BUILD_PGSQL=ON -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_CONFIG=/usr/bin/pg_config -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/17/server" -DPYTHON_EXECUTABLE=/usr/bin/python3.13 ../
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_USE_URF=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DRDK_BUILD_PGSQL=ON -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_CONFIG=/usr/bin/pg_config -DPostgreSQL_TYPE_INCLUDE_DIR=/usr/include/postgresql/17/server -DPYTHON_EXECUTABLE=/usr/bin/python3.13 ../ ..
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Inchi: /usr/lib/x86_64-linux-gnu/libinchi.so
-- Found Python3: /usr/bin/python3 (found version "3.13.2") found components: Interpreter Development.Module NumPy
Python Install directory /usr/lib/python3.13/site-packages
nbval not found, disabling the jupyter tests
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found PostgreSQL: /usr/lib/x86_64-linux-gnu/libpq.so (found version "17.4")
== Using strict rotor definition
-- maeparser include dir set as '/usr/include'
-- maeparser libraries set as '/usr/lib/x86_64-linux-gnu/libmaeparser.so'
-- coordgen include dir set as /usr/include
-- coordgen libraries set as '/usr/lib/x86_64-linux-gnu/libcoordgen.so'
-- Found Python3: /usr/bin/python3 (found version "3.13.2") found components: Interpreter
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1")
-- Found Cairo: /usr/include/cairo
-- Found Freetype: /usr/lib/x86_64-linux-gnu/libfreetype.so (found version "2.13.3")
postgres: /usr/include/postgresql;/usr/include/postgresql/17/server
CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (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.
CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (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.
CMake Warning (dev) at Code/PgSQL/rdkit/CMakeLists.txt:303 (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.
-- Configuring done (1.8s)
-- Generating done (1.1s)
CMake Warning:
Manually-specified variables were not used by the project:
Boost_NO_BOOST_CMAKE
CATCH_DIR
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
PYTHON_EXECUTABLE
-- Build files have been written to: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu
for v in $(pg_buildext supported-versions); do \
(mkdir -p Code/PgSQL/rdkit/build-$v && cd Code/PgSQL/rdkit/build-$v && cmake -DPostgreSQL_CONFIG=/usr/lib/postgresql/$v/bin/pg_config -DRDK_PGSQL_STATIC=OFF -DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/$v/server" -DCMAKE_VERBOSE_MAKEFILE=1 -DRDKit_CodeDir=../../../Code ../); \
done
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PostgreSQL: /usr/lib/x86_64-linux-gnu/libpq.so (found version "17.4")
postgres: /usr/include/postgresql;/usr/include/postgresql/17/server
CMake Warning (dev) at CMakeLists.txt:303 (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.
CMake Warning (dev) at CMakeLists.txt:303 (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.
CMake Warning (dev) at CMakeLists.txt:303 (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.
-- Configuring done (0.5s)
-- Generating done (0.0s)
-- Build files have been written to: /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17
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debian/rules override_dh_auto_build
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dh_auto_build
cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/IntegerStringChromosomePolicy.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o -MF CMakeFiles/RDGeneral.dir/types.cpp.o.d -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/types.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/util/Util.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDStreams/streams.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/versions.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/Cluster/Murtagh/hcdriver.c
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/Chromosome.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/LocaleSwitcher.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/util/RandomUtil.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_main.cpp
[ 1%] Built target inchi_support
[ 1%] Linking C shared library ../../../../lib/libRDKithc.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2024.09.6 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2024.09.6 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 1%] Built target hc
[ 2%] Linking CXX shared library ../../lib/libRDKitga.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1
[ 2%] Linking CXX static library librdkitCatch.a
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ga.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2024.09.6 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2024.09.6 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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[ 2%] Built target rdkitCatch
[ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2024.09.6 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so
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[ 2%] Built target RDStreams
[ 2%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDGeneral.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 2%] Built target RDGeneral
make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DiscreteDistMat.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVect.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -MF CMakeFiles/testMatrices.dir/testMatrices.cpp.o.d -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/testMatrices.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_logs.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogEntry.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/MaxMinPicker.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/MultiFPBReader.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/DistPicker.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/HierarchicalClusterPicker.cpp
[ 5%] Linking CXX executable testMatCalc
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatCalc.dir/link.d CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 5%] Built target testMatCalc
[ 5%] Linking CXX executable testConcurrentQueue
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testConcurrentQueue.dir/link.d CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1
[ 5%] Built target testConcurrentQueue
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/EigenSolvers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 5%] Built target EigenSolvers
[ 6%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2024.09.6 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2024.09.6 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 6%] Built target SimDivPickers
make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/testPickers.cpp
[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2024.09.6 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so
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[ 7%] Built target Catalogs
[ 8%] Linking CXX executable logTestsCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 8%] Built target logTestsCatch
[ 8%] Linking CXX executable testMatrices
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 8%] Built target testMatrices
[ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2024.09.6 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 8%] Built target DataStructs
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform2D.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/testDatastructs.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/testFPB.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -MF CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o.d -o CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/catch_tests.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/point.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform3D.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/testMultiFPB.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformGrid3D.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformRealValueGrid3D.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/GridUtils.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so
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make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_SparseBV.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_BitOps.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_FPB.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_Utils.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Features && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Features/testFeatures.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/AlignPoints.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/catch_tests.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/testTransforms.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryAtom.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/UniformGrid3D.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Atom.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/Point.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryBond.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/rdGeometry.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/FreeChemicalFeature.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Bond.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ROMol.cpp
[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RWMol.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2024.09.6 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so
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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/Clustering.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
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[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.cpp
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[ 16%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o
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1292 | void findRingFamilies(const ROMol &mol) {
| ~~~~~~~~~~~~~^~~
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/AddHs.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Conformer.cpp
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[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/new_canon.cpp
[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstanceGroup.cpp
[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindStereo.cpp
[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MonomerInfo.cpp
[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/NontetrahedralStereo.cpp
[ 20%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKithc.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atropisomers.cpp.o -MF CMakeFiles/GraphMol.dir/Atropisomers.cpp.o.d -o CMakeFiles/GraphMol.dir/Atropisomers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Atropisomers.cpp
[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/WedgeBonds.cpp
[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o -MF CMakeFiles/GraphMol.dir/MolProps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolProps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProps.cpp
[ 20%] Linking CXX executable testChemicalFeatures
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[ 20%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1
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[ 20%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdInfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 20%] Built target rdInfoTheory
[ 20%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 20%] Built target rdGeometry
[ 20%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cDataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 20%] Built target cDataStructs
[ 20%] Linking CXX shared library ../../lib/libRDKitGraphMol.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GraphMol.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2024.09.6 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/Atropisomers.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o CMakeFiles/GraphMol.dir/MolProps.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 20%] Built target GraphMol
make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CXSmilesOps.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -MF CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o.d -o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smarts.tab.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/lex.yysmarts.cpp
[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp
[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNAttribs.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/lex.yysmiles.cpp
[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp
[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp
[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.cpp
[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.cpp
[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o
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[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp
[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp
[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/BFGSOpt.cpp
[ 28%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 28%] Built target MolCatalog
make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 28%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp
[ 28%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1
[ 28%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Subgraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 28%] Built target PartialCharges
make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake "--color="
[ 28%] Built target Subgraphs
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 28%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp
[ 28%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2024.09.6 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 28%] Built target Optimizer
make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend
make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o
[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o
[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o
[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o
[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/testOptimizer.cpp
[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.cpp
[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraint.cpp
[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o
[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/PositionConstraint.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/TorsionConstraint.cpp
[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o
[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleBend.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/BondStretch.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Nonbonded.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.cpp
[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversion.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversions.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionAngle.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Params.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Utils.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Utils.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleBend.cpp
[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/OopBend.cpp
[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Nonbonded.cpp
[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionAngle.cpp
[ 30%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so
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[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Params.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.cpp
[ 31%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructUtils.cpp
[ 31%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 31%] Built target MolTransforms
make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend
make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake "--color="
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make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build
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make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 31%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o
[ 31%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp
[ 31%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp
[ 31%] Linking CXX executable testOptimizer
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testOptimizer.dir/link.d CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdPartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 32%] Built target rdPartialCharges
[ 32%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2024.09.6 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 32%] Built target SLNParse
make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 32%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp
[ 32%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 32%] Built target rdtrajectory
[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1
[ 32%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 32%] Built target rdCIPLabeler
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 32%] Built target rdqueries
[ 32%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1
[ 33%] Linking CXX shared library ../../lib/libRDKitForceField.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 33%] Built target ShapeHelpers
make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 33%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2024.09.6 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 33%] Built target ForceField
[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 33%] Built target rdMolCatalog
[ 33%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 33%] Built target MolInterchange
make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 33%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp
[ 33%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1
[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 33%] Built target rdSLNParse
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SmilesParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/cptest.cpp
[ 34%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/test2.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/itertest.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o -MF CMakeFiles/testSubgraphs1.dir/test1.cpp.o.d -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/test1.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_queries.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/memtest1.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o -MF CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o.d -o CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/v2catch_tests.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -MF CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o.d -o CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_molbundle.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/test2.cpp
[ 34%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o
[ 34%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/catch_tests.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/test1.cpp
[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1
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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/test.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp
[ 35%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp
[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o
[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairs.cpp
[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp
[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatGenerator.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp
[ 35%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Filters.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.cpp
[ 35%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o
[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smatest.cpp
[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o
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[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o
[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o
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[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o
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[ 36%] Linking CXX executable graphmolcpTest
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[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o
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[ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o
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[ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so
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[ 36%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o
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[ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/subgraphsCatch.dir/link.d CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -o subgraphsCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 36%] Built target subgraphsCatch
[ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o
[ 36%] Linking CXX executable graphmolIterTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolIterTest.dir/link.d CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp
[ 36%] Linking CXX executable testSubgraphs2
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[ 37%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp
[ 37%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.cpp
[ 37%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp
[ 37%] Linking CXX executable molbundleTestsCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1
[ 37%] Linking CXX executable testSubgraphs1
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molbundleTestsCatch.dir/link.d CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 37%] Built target molbundleTestsCatch
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubgraphs1.dir/link.d CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 37%] Linking CXX executable moliteratorTestsCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1
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[ 37%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so
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make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build
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[ 37%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o
[ 37%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/test1.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp
[ 37%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Abbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2024.09.6 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so
[ 37%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 37%] Built target Abbreviations
make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 37%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 37%] Built target FragCatalog
[ 37%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1
[ 37%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so
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[ 37%] Built target MolChemicalFeatures
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color="
[ 37%] Built target MolAlign
make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/CoordGen/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake "--color="
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[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o
[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o
[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o
[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o
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[ 41%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o
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[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o
[ 41%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o
[ 41%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistViolationContrib.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContrib.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistViolationContribs.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContribs.cpp
[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o
[ 41%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o
[ 41%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/catch_tests.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap/ForceField.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInteractionFields_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERACTIONFIELDS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -MF CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o.d -o CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2024.09.6 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 41%] Built target Fingerprints
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color="
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make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp
[ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp
[ 41%] Linking CXX executable testReducedGraphs
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReducedGraphs.dir/link.d CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 41%] Built target testReducedGraphs
[ 41%] Linking CXX executable graphmolqueryTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1
[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 41%] Built target graphmolqueryTest
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 41%] Built target rdReducedGraphs
[ 41%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 41%] Built target FilterCatalog
make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color="
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make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o
[ 42%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp
[ 42%] Linking CXX executable testSLNParse
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSLNParse.dir/link.d CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 42%] Built target testSLNParse
[ 43%] Linking CXX executable ForceFieldsCatch
[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ForceFieldsCatch.dir/link.d CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -o ForceFieldsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 43%] Built target rdMolChemicalFeatures
[ 43%] Built target ForceFieldsCatch
[ 43%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.6 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so
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make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color="
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make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o
[ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o
[ 43%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/DistGeom.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp
[ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.cpp
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 43%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/testDistGeom.cpp
[ 43%] Linking CXX executable smaTest1
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smaTest1.dir/link.d CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 43%] Built target smaTest1
[ 43%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 43%] Built target rdCoordGen
[ 43%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInteractionFields.so.1 -o ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so
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[ 43%] Built target MolInteractionFields
make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/DependInfo.cmake "--color="
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[ 44%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp
[ 44%] Linking CXX executable testDistGeom
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so
[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1
[ 44%] Built target testDistGeom
[ 44%] Linking CXX shared library ../../../lib/libRDKitDepictor.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 44%] Built target rdForceFieldHelpers
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 44%] Built target rdAbbreviations
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2024.09.6 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so
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[ 44%] Built target Depictor
make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend
make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/INCHI-API /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/RDInchiLib.dir/DependInfo.cmake "--color="
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[ 44%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o
[ 44%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o
[ 44%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o
[ 44%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/ChemTransforms.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp
[ 44%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDInchiLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDINCHILIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o -MF CMakeFiles/RDInchiLib.dir/inchi.cpp.o.d -o CMakeFiles/RDInchiLib.dir/inchi.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/INCHI-API/inchi.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/MolFragmenter.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/normalize.cpp
[ 44%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/hashfunctions.cpp
[ 44%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target rdForceField
[ 44%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target DistGeom
[ 44%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1
[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target DistGeomHelpers
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target rdMHFPFingerprint
[ 44%] Linking CXX shared library ../../../lib/libRDKitMolHash.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2024.09.6 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target MolHash
make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color="
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make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp
[ 44%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1
[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDInchiLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2024.09.6 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2024.09.6 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so
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[ 44%] Built target RDInchiLib
make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdinchi_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -MF CMakeFiles/rdinchi.dir/pyInchi.cpp.o.d -o CMakeFiles/rdinchi.dir/pyInchi.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/INCHI-API/Wrap/pyInchi.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target rdFingerprintGenerator
[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target rdDepictor
[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target rdMolHash
[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMIF.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMIF.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMIF.so CMakeFiles/rdMIF.dir/rdMIF.cpp.o ../../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Built target rdMIF
[ 44%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so
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make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o
[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o
[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o
[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o
[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o
[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileParser.cpp
[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/Mol2FileParser.cpp
[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.cpp
[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupWriting.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileWriter.cpp
[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SDMolSupplier.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SDWriter.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SmilesWriter.cpp
[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/TDTMolSupplier.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/TDTWriter.cpp
[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/TplFileParser.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/TplFileWriter.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/PDBParser.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/PDBWriter.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CMLWriter.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/XYZFileWriter.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/XYZFileParser.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/MaeMolSupplier.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MaeWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MaeWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MaeWriter.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/ProximityBonds.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceParsers.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/SequenceWriters.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/SVGParser.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/PNGParser.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp
[ 48%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdinchi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 48%] Built target rdinchi
[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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[ 48%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FileParsers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so
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[ 48%] Built target FileParsers
make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testTpls.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testSequence.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o.d -o CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_organometallics.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionPickler.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_graphmol.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_sgroups.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -MF CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o.d -o CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testAtropisomers.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testChirality.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testMolWriter.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testPickler.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ChemReactions/MDLParser.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/file_parsers_catch.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/catch_tests.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testMolBundle.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -MF CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o.d -o CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_molops.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/test-valgrind.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/testMMFFForceField.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/molopstest.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/catch_tests.cpp
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testMolSupplier.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/hanoitest.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testPicklerGlobalSettings.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -MF CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o.d -o CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_adjustquery.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_canon.cpp
make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o -MF CMakeFiles/smiTest1.dir/test.cpp.o.d -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/test.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/DaylightParser.cpp
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/test1.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/testUFFForceField.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/pickleTestsCatch.dir/catch_pickles.cpp.o -MF CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o.d -o CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_pickles.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/chiralityTestsCatch.dir/catch_chirality.cpp.o -MF CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o.d -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_chirality.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Reaction.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testMol2ToMol.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/resMolSupplierTest.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/testDepictor.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testGeneralFileReader.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testSGroup.cpp
[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/test1.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testPropertyLists.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 52%] Built target testExtendedStereoParsing
[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp
[ 52%] Linking CXX executable testSquiggleDoubleBonds
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.dir/link.txt --verbose=1
make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color="
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSquiggleDoubleBonds.dir/link.d CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -o testSquiggleDoubleBonds ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
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make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o
[ 52%] Built target testSquiggleDoubleBonds
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp
[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionUtils.cpp
[ 53%] Linking CXX executable testTplParser
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 53%] Built target testTplParser
make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp
[ 53%] Linking CXX executable testAtropisomers
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1
[ 53%] Linking CXX executable molopsTestsCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 53%] Built target testAtropisomers
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/MoleculeParser.cpp
[ 53%] Built target molopsTestsCatch
[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionRunner.cpp
make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color="
[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PreprocessRxn.cpp
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp
[ 53%] Linking CXX executable testMultithreadedMolSupplier
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1
[ 53%] Linking CXX executable graphmolOrganometallicsCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1
[ 53%] Linking CXX executable resMolSupplierTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1
[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/SanitizeRxn.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolOrganometallicsCatch.dir/link.d CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -o graphmolOrganometallicsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 53%] Built target testMultithreadedMolSupplier
[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o
[ 53%] Built target graphmolOrganometallicsCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PNGParser.cpp
make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color="
[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/CDXMLParser.cpp
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/obj-x86_64-linux-gnu'
[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/connectTheDots_catch.cpp
[ 54%] Linking CXX executable testGeneralFileReader
[ 54%] Linking CXX executable nontetrahedralCatch
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color="
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[ 54%] Linking CXX executable graphmoltestPicklerGlobalSetting
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1
[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp
[ 54%] Linking CXX executable molBundleTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
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[ 54%] Built target testGeneralFileReader
make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color="
[ 54%] Built target nontetrahedralCatch
make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color="
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[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp
[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.d CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molBundleTest.dir/link.d CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 54%] Built target graphmoltestPicklerGlobalSetting
[ 54%] Built target molBundleTest
make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color="
[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp
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[ 54%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/test1.cpp
[ 54%] Linking CXX executable testUFFForceField
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceField.dir/link.d CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
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[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o
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[ 54%] Linking CXX executable hanoiTest
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[ 54%] Linking CXX executable pickleTestsCatch
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make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickleTestsCatch.dir/link.d CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color="
[ 54%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o
[ 54%] Built target hanoiTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/catch_tests.cpp
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[ 54%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o
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[ 54%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 54%] Linking CXX executable XYZFileParserCatchTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1
[ 55%] Linking CXX executable testDepictor
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[ 55%] Built target connectTheDotsTest
[ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/BCUT.cpp
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[ 55%] Built target testDepictor
make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake "--color="
[ 55%] Built target XYZFileParserCatchTest
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 55%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp
[ 55%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/test1.cpp
[ 55%] Linking CXX executable graphmolAdjustQueryCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1
[ 55%] Linking CXX executable v2FileParsersCatchTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1
make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 55%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolAdjustQueryCatch.dir/link.d CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 55%] Built target graphmolAdjustQueryCatch
[ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolDescriptors.cpp
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[ 55%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Lipinski.cpp
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[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o
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[ 56%] Linking CXX executable multithreadedSupplierCatchTest
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[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o
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[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o
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[ 56%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp
[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o
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[ 56%] Linking CXX executable cdxmlParserCatchTest
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[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/USRDescriptor.cpp
[ 58%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o
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[ 58%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o
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[ 58%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.cpp.o
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[ 59%] Linking CXX executable testMMFFForceField
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[ 59%] Linking CXX executable testMHFPFingerprint
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color="
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[ 59%] Built target testMHFPFingerprint
[ 59%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/catch_tests.cpp
[ 59%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/EEM.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceField.dir/link.d CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color="
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[ 60%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -MF CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o.d -o CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp
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[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PBF.cpp
[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PMI.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
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make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/WHIM.cpp
[ 61%] Built target testMolSupplier
[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/CoulombMat.cpp
make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp
make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 61%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
[ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1
make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfragcatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend
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make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/catch_tests.cpp
[ 62%] Linking CXX executable graphmoltestChirality
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1
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[ 62%] Linking CXX executable depictorCatch
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/test1.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/FMCS.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/catch_tests.cpp
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[ 63%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalMCES.cpp
[ 64%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp
[ 64%] Linking CXX executable testSubstructMatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 64%] Built target testSubstructMatch
[ 64%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.cpp
[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalCluster.cpp
[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp
[ 65%] Linking CXX executable forceFieldHelpersCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 65%] Linking CXX executable substructTestCatch
[ 65%] Built target forceFieldHelpersCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1
[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 65%] Built target substructTestCatch
[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -MF CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.cpp
[ 65%] Linking CXX executable molTransformsTestCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTransformsTestCatch.dir/link.d CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -o molTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 65%] Built target molTransformsTestCatch
[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalResult.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.cpp
[ 65%] Linking CXX executable testMolTransforms
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1
[ 65%] Linking CXX executable testMMFFForceFieldHelpersMultiThread
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 65%] Built target testMolTransforms
make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend
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[ 65%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp
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[ 66%] Linking CXX executable testChemTransforms
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[ 66%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/test1.cpp
[ 66%] Linking CXX executable testShapeHelpers
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1
[ 66%] Linking CXX executable fpGenTestCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testShapeHelpers.dir/link.d CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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[ 66%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/PositionVariation.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 66%] Built target fpGenTestCatch
[ 66%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Synthon.cpp
[ 66%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.cpp
[ 66%] Linking CXX executable molAlignCatchTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1
[ 66%] Linking CXX executable chemTransformsTestCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molAlignCatchTest.dir/link.d CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 66%] Built target molAlignCatchTest
[ 66%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chemTransformsTestCatch.dir/link.d CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
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[ 66%] Linking CXX executable smiTest1
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1
[ 66%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/LinkNode.cpp
[ 66%] Built target chemTransformsTestCatch
make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 66%] Linking CXX executable testMolAlign
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1
[ 66%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/molinterchange_catch.cpp
[ 66%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp
[ 66%] Linking CXX executable testMolCatalog
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake "--color="
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
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make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 66%] Built target testMolCatalog
make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake "--color="
[ 66%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdmolops.cpp
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 66%] Built target smiTest1
[ 66%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/catch_tests.cpp
[ 66%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/RepeatUnit.cpp
[ 66%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolOps.cpp
[ 66%] Linking CXX shared library ../../../lib/libRDKitMMPA.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1
[ 66%] Linking CXX executable testMMFFForceFieldHelpers
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1
[ 66%] Linking CXX executable fpTestCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2024.09.6 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so
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[ 66%] Built target MMPA
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[ 67%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so
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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Deprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2024.09.6 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2024.09.6 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinWriter.cpp
[ 67%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.cpp
[ 67%] Linking CXX executable trajectoryTest
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[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/MolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.cpp
[ 68%] Linking CXX executable testFingerprintGenerators
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[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp
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[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o
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[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp
[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Metal.cpp
make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/deprotectTest.cpp
[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Normalize.cpp
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[ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so
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[ 69%] Built target MolProcessing
[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2024.09.6 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so
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[ 70%] Built target FMCS
make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake "--color="
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 70%] Built target graphmolTestsCatch
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeTest1.dir/link.d CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 70%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp
[ 70%] Built target molInterchangeTest1
[ 70%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp
[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp
[ 70%] Linking CXX executable testFingerprints
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 70%] Built target testFingerprints
make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 70%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -MF CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o.d -o CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/processing_tests.cpp
[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Tautomer.cpp
[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Fragment.cpp
[ 70%] Linking CXX executable testReactionFingerprints
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[ 70%] Linking CXX executable molInterchangeCatchTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1
[ 70%] Built target testReactionFingerprints
[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.cpp
[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp
[ 70%] Linking CXX executable testAbbreviations
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[ 70%] Linking CXX executable chiralityTestsCatch
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[ 70%] Linking CXX executable testMMPA
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1
[ 70%] Built target molInterchangeCatchTest
[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp
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make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 70%] Linking CXX executable testDistGeomHelpers
[ 70%] Built target testMMPA
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1
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[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp
[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawShape.cpp
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[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp
[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp
make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 70%] Building CXX object Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolProcessing_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -MF CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o.d -o CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp
[ 70%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color="
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[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/testFMCS_Unit.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1
[ 70%] Built target MolEnumerator
[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 70%] Built target rdMMPA
[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp
[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp
[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp
[ 71%] Linking CXX executable testEnumeration
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1
[ 71%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1
[ 71%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 71%] Built target testEnumeration
[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp
[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so
[ 71%] Linking CXX executable testMIF
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMIF.dir/link.txt --verbose=1
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRascalMCES.so.1 -o ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so
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[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o
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[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp
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[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/mces_catch.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.dir/link.txt --verbose=1
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so
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[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp
[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp
[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp
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[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/enumerator_catch.cpp
[ 73%] Linking CXX executable fileParsersTest1
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp
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In file included from /usr/include/c++/14/vector:62,
from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15:
In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]',
inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30,
inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42,
inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<int*, vector<int> >; _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<int*, vector<int> >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7,
inlined from 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<int*, std::vector<int> >; _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<int*, vector<int> >; _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<int*, vector<int> >; _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<int*, std::vector<int> >; _Tp = int; _Alloc = std::allocator<int>]' 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<int*, std::vector<int> >; <template-parameter-2-2> = void; _Tp = int; _Alloc = std::allocator<int>]' at /usr/include/c++/14/bits/stl_vector.h:1488:19,
inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector<RDKit::DrawColour>&, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&) const' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32:
/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=]
452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/vector:63:
In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]',
inlined from 'static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28,
inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator<int>]' 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<int*, std::vector<int> >; _Tp = int; _Alloc = std::allocator<int>]' 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<int*, std::vector<int> >; <template-parameter-2-2> = void; _Tp = int; _Alloc = std::allocator<int>]' at /usr/include/c++/14/bits/stl_vector.h:1488:19,
inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector<RDKit::DrawColour>&, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&) const' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32:
/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new'
151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
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[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -MF CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o.d -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testCoulombMat.cpp
make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/catch_tests.cpp
[ 77%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDescriptors_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -MF CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o.d -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp
[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolProcessing.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolProcessing.so CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o ../../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDStreams.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 77%] Built target rdMolProcessing
make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1
[ 77%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDeprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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[ 77%] Linking CXX executable testRascalCluster
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 77%] Built target testRascalCluster
[ 77%] Linking CXX executable testATF
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1
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make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 77%] Built target testATF
[ 77%] Linking CXX executable testBCUT
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testBCUT.dir/link.d CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 77%] Built target testBCUT
[ 77%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 CMakeFiles/MolStandardize.dir/Pipeline.cpp.o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/TautomerQuery.cpp
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[ 80%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Metal.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp
[ 80%] Built target testPBF
[ 80%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEEM.dir/link.d CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDF.dir/link.d CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 80%] Built target testRDF
[ 80%] Built target testEEM
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testWHIM.dir/link.d CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 80%] Built target testWHIM
[ 80%] Linking CXX executable testAUTOCORR3D
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[ 80%] Linking CXX executable graphmolMolOpsTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAUTOCORR3D.dir/link.d CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 80%] Built target testAUTOCORR3D
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 80%] Built target graphmolMolOpsTest
[ 80%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so
[ 80%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1
[ 80%] Built target MarvinParser
make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend
make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend
make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDFcustom.dir/link.d CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 82%] Built target testRDFcustom
[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Atom.cpp
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[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Bond.cpp
[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so
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[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1
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[ 83%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o
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[ 83%] Built target rdMolEnumerator
[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Mol.cpp
[ 83%] Linking CXX executable molStandardizeSmallTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 83%] Built target molStandardizeSmallTest
[ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPMol.cpp
[ 83%] Linking CXX executable testRascalMCES
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1
[ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalMCES.dir/link.d CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 85%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1
[ 85%] Built target testRascalMCES
[ 85%] Built target rdFMCS
make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdmolfiles.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Conformer.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 86%] Linking CXX executable descriptorsTestCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1
[ 86%] Built target O3AAlign
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/RingInfo.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 86%] Built target descriptorsTestCatch
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/EditableMol.cpp
[ 86%] Linking CXX executable molNormalizeTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1
[ 86%] Linking CXX executable molFragmentTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1
[ 86%] Linking CXX executable testFMCS
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molNormalizeTest.dir/link.d CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 86%] Linking CXX executable molChargeTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1
[ 86%] Built target molNormalizeTest
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MonomerInfo.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molFragmentTest.dir/link.d CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFMCS.dir/link.d CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 86%] Built target molChargeTest
[ 86%] Built target molFragmentTest
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp
[ 86%] Built target testFMCS
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolBundle.cpp
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/StereoGroup.cpp
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SubstanceGroup.cpp
[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp
[ 87%] Linking CXX executable molValidateTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molValidateTest.dir/link.d CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 87%] Built target molValidateTest
[ 87%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1
[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MaeMolSupplier.cpp
[ 87%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1
[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MaeWriter.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolops.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 88%] Built target rdmolops
[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Chirality.cpp
[ 88%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1
[ 88%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 88%] Built target MolDraw2D
[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPLabeler.cpp
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 89%] Built target ScaffoldNetwork
[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SDMolSupplier.cpp
[ 89%] Built target TautomerQuery
[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.cpp
[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Digraph.cpp
[ 89%] Linking CXX executable rxnTestCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1
[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/TDTMolSupplier.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rxnTestCatch.dir/link.d CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 89%] Built target rxnTestCatch
[ 90%] Linking CXX executable testMolEnumerator
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1
[ 90%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Node.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 90%] Built target testMolEnumerator
[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SmilesMolSupplier.cpp
[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SmilesWriter.cpp
[ 90%] Linking CXX executable molStandardizeTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 90%] Built target molStandardizeTest
[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SDWriter.cpp
[ 90%] Linking CXX executable testDescriptors
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1
make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 90%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp
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[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/TDTWriter.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake "--color="
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[ 90%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp
[ 90%] Linking CXX executable testMrvToMol
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[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/PDBWriter.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGenericGroups.dir/link.d CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
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[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp
[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp
[ 91%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o
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[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o
[ 93%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp
[ 93%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp
[ 93%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.cpp
In file included from /usr/include/boost/shared_ptr.hpp:17,
from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12,
from /usr/include/boost/python/converter/arg_to_python.hpp:15,
from /usr/include/boost/python/call.hpp:15,
from /usr/include/boost/python/object_core.hpp:14,
from /usr/include/boost/python/args.hpp:22,
from /usr/include/boost/python.hpp:11,
from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32:
In copy constructor 'boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]',
inlined from 'std::vector<std::vector<boost::shared_ptr<RDKit::ROMol> > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25:
/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr<RDKit::ROMol>*)((char*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)).boost::shared_ptr<RDKit::ROMol>::px' may be used uninitialized [-Wmaybe-uninitialized]
459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn )
| ~~^~
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector<std::vector<boost::shared_ptr<RDKit::ROMol> > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]':
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '<anonymous>' declared here
55 | RDKit::ROMOL_SPTR mol = python::extract<RDKit::ROMOL_SPTR>(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<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72,
inlined from 'std::vector<std::vector<boost::shared_ptr<RDKit::ROMol> > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202409.6/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*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized]
438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_)
| ~~^~~
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector<std::vector<boost::shared_ptr<RDKit::ROMol> > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]':
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '<anonymous>' declared here
55 | RDKit::ROMOL_SPTR mol = python::extract<RDKit::ROMOL_SPTR>(bbs[i][j]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In copy constructor 'boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]',
inlined from 'std::vector<std::vector<boost::shared_ptr<RDKit::ROMol> > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25:
/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr<RDKit::ROMol>*)((char*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)).boost::shared_ptr<RDKit::ROMol>::px' may be used uninitialized [-Wmaybe-uninitialized]
459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn )
| ~~^~
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector<std::vector<boost::shared_ptr<RDKit::ROMol> > > RDKit::ConvertToVect(T) [with T = boost::python::list]':
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '<anonymous>' declared here
55 | RDKit::ROMOL_SPTR mol = python::extract<RDKit::ROMOL_SPTR>(bbs[i][j]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)',
inlined from 'boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72,
inlined from 'std::vector<std::vector<boost::shared_ptr<RDKit::ROMol> > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.6/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*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized]
438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_)
| ~~^~~
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector<std::vector<boost::shared_ptr<RDKit::ROMol> > > RDKit::ConvertToVect(T) [with T = boost::python::list]':
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '<anonymous>' declared here
55 | RDKit::ROMOL_SPTR mol = python::extract<RDKit::ROMOL_SPTR>(bbs[i][j]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp
[ 94%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupData.cpp
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[ 94%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/catch_tests.cpp
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[ 94%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o
[ 94%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp
[ 94%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp
[ 94%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o
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[ 95%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o
[ 95%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule6.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp
[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp
[ 95%] Linking CXX executable moldraw2DRxnTest1
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 95%] Built target moldraw2DRxnTest1
[ 95%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1
[ 95%] Linking CXX executable testCIPLabeler
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 95%] Built target rdMolStandardize
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCIPLabeler.dir/link.d CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 95%] Built target testCIPLabeler
[ 95%] Linking CXX executable testO3AAlign
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1
[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testO3AAlign.dir/link.d CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 95%] Built target testO3AAlign
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDescriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 95%] Built target rdMolDescriptors
[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 95%] Built target rdMolAlign
[ 95%] Linking CXX executable tautomerQueryTestCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1
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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so
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[ 95%] Built target tautomerQueryTestCatch
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[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/low_gist.c
[ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp
[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o
[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o
[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o
[ 95%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o
[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o
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[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o
[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_op.c
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/PatternFactory.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/guc.c
[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/cache.c
[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o
[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/mol_op.c
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rdkit_gist.c
[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_gist.c
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_gin.c
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bitstring.c
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rdkit_io.c
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rxn_op.c
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/sfp_op.c
[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 96%] Built target rdTautomerQuery
[ 96%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1
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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testScaffoldNetwork.dir/link.d CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)':
/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:38: warning: unused parameter 'data' [-Wunused-parameter]
1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery,
| ~~~~~~~^~~~
/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:49: warning: unused parameter 'isQuery' [-Wunused-parameter]
1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery,
| ~~~~~^~~~~~~
/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1628:44: warning: unused parameter 'bitFlags' [-Wunused-parameter]
1628 | unsigned int bitFlags) {
| ~~~~~~~~~~~~~^~~~~~~~
[ 96%] Built target testScaffoldNetwork
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o -MF CMakeFiles/gaExample.dir/GaExample.cpp.o.d -o CMakeFiles/gaExample.dir/GaExample.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/GaExample.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp
[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o
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cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
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[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target rdChemReactions
[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target rdGeneralizedSubstruct
[ 97%] Linking CXX executable gaExample
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1
[ 97%] Linking CXX executable testRGroupDecompInternals
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target gaExample
[ 97%] Linking CXX executable generalizedSubstructCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target testRGroupDecompInternals
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/generalizedSubstructCatch.dir/link.d CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target generalizedSubstructCatch
[ 97%] Linking CXX shared library librdkit.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/lib /usr/lib/x86_64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/sql
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/data
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/expected
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target rdkit
[ 97%] Linking CXX executable moldraw2DTest1
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target moldraw2DTest1
[ 97%] Linking CXX executable rgroupCatchTests
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1
[ 97%] Built target rgroupCatchTests
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target rdMolDraw2D
[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitga.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target rdRGroupDecomposition
[ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 97%] Built target SubstructLibrary
make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend
make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend
make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend
make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build
make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build
make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o
[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp
[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o
[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/catch_tests.cpp
[ 99%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp
[ 99%] Linking CXX executable testRGroupDecomp
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 99%] Built target testRGroupDecomp
[ 99%] Linking CXX executable substructLibraryCatchTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1
[ 99%] Linking CXX executable substructLibraryTest
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 99%] Built target substructLibraryTest
[ 99%] Built target substructLibraryCatchTest
[ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1
/usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()':
./obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/./Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp:306:(.text+0x7b4f): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 99%] Built target testSynthonSpaceSubstructureSearch
[ 99%] Linking CXX executable moldraw2DTestCatch
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[ 99%] Built target moldraw2DTestCatch
[100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so
cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
[100%] Built target rdSubstructLibrary
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolData3Ddescriptors.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolDescriptors.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolDescriptors3D.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolSurf.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolSurf.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MQN.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MQN.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/OxidationNumbers.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/OxidationNumbers.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PBF.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PMI.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Property.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Property.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RDF.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RDF.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RegisterDescriptor.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RegisterDescriptor.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/USRDescriptor.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/USRDescriptor.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/WHIM.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/WHIM.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/details.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/details.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DetermineBonds/DetermineBonds.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DetermineBonds/DetermineBonds.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParsers.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParsers.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParserUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParserUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/GeneralFileReader.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/GeneralFileReader.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MaestroProperties.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MaestroProperties.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupWriting.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupWriting.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.v1API.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.v1API.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolWriters.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolWriters.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/PNGParser.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/PNGParser.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/ProximityBonds.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/ProximityBonds.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceParsers.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceParsers.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceWriters.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceWriters.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalog.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalog.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Filters.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Filters.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairGenerator.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairGenerator.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairs.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MACCS.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MACCS.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/RDKitFPGenerator.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/RDKitFPGenerator.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Composition2N.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Composition2N.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/DebugTrace.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/DebugTrace.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/DuplicatedSeedCache.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/DuplicatedSeedCache.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/FMCS.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/FMCS.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Graph.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Graph.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MatchTable.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MatchTable.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MaximumCommonSubgraph.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MaximumCommonSubgraph.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Seed.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Seed.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SeedSet.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SeedSet.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructureCache.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructureCache.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Target.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Target.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/TargetMatch.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/TargetMatch.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/FFConvenience.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/FFConvenience.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogEntry.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogEntry.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatGenerator.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatGenerator.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatParams.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatParams.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragFPGenerator.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragFPGenerator.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/XQMol.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/XQMol.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/GenericGroups.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/GenericGroups.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GraphMol.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GraphMol.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/O3AAlignMolecules.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/O3AAlignMolecules.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolBundle.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolBundle.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalog.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalog.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogEntry.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogEntry.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogParams.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogParams.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/FeatureParser.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/FeatureParser.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/AtomSymbol.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/AtomSymbol.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawShape.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawShape.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextCairo.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextCairo.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFT.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFT.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Dr/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h:233: warning: unbalanced grouping commands
awTextFTCairo.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTJS.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTJS.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextJS.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextJS.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextNotFT.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextNotFT.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextSVG.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextSVG.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DJS.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DJS.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/StringRect.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/StringRect.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/LinkNode.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/LinkNode.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h...
Prepro/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h:489: warning: unbalanced grouping commands
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h:747: warning: unbalanced grouping commands
cessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/mf.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/mf.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/MolHash.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/MolHash.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/nmmolhash.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/nmmolhash.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/details.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/details.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/MolInterchange.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/MolInterchange.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolPickler.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolPickler.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/MolProcessing.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/MolProcessing.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Fragment.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Fragment.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Metal.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Metal.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/MolStandardize.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/MolStandardize.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Normalize.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Normalize.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Tautomer.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Tautomer.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Validate.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Validate.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/MolTransforms.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/MolTransforms.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MonomerInfo.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MonomerInfo.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/new_canon.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/new_canon.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerCharges.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerCharges.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerParams.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerParams.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PeriodicTable.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryAtom.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryBond.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryBond.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalClusterOptions.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalClusterOptions.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalDetails.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalDetails.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalMCES.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalMCES.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalOptions.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalOptions.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RDKitBase.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RDKitBase.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RDKitQueries.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RDKitQueries.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Resonance.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Resonance.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupCore.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupCore.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupData.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupData.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupGa.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupGa.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupMatch.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupMatch.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupScore.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupScore.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RingInfo.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RingInfo.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Rings.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Rings.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ROMol.h...
Parsing file /build/reproducible-path/rdkit-202409.6//build/reproducible-path/rdkit-202409.6/Code/GraphMol/ROMol.h:416: warning: unbalanced grouping commands
Code/GraphMol/ROMol.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RWMol.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RWMol.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SanitException.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SanitException.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/detail.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/detail.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeEncoder.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeEncoder.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNAttribs.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNAttribs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParse.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParse.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParseOps.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmartsWrite.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParse.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParseOps.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParseOps.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StereoGroup.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Pattern.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/ReCharge.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Stereo.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/StripSmallFragments.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/StructCheckerOptions.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker/Tautomer.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstanceGroup.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/PatternFactory.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSet.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/TautomerQuery.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/Snapshot.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogEntry.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogParams.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitOps.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVect.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVect.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVects.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVectUtils.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DatastructsException.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DatastructsStreamOps.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DiscreteDistMat.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/DiscreteValueVect.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/ExplicitBitVect.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/ExplicitBitVect.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/FPBReader.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/MultiFPBReader.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/SparseBitVect.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataStructs/SparseIntVect.h...
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Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/EqualityQuery.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/GreaterEqualQuery.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Query/NullQueryAlgebra.h...
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Parsing file /build/reproducible-path/rdkit-202409.6/Code/Query/OrQuery.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/CorrMatGenerator.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/InfoBitRanker.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/InfoGainFuncs.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/MetricFuncs.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/LeaderPicker.h...
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Preprocessing /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDExportMacros.h...
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Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistViolationContribs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContrib.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContrib.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContribs.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContribs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/DistGeom/TriangleSmooth.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/DistGeom/TriangleSmooth.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/Contrib.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/Contrib.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleBend.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleBend.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Contribs.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Contribs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/DistanceConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/DistanceConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Nonbonded.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Nonbonded.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/OopBend.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/OopBend.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Params.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Params.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/PositionConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/PositionConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionAngle.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionAngle.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/PositionConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/PositionConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/TorsionConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/TorsionConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleBend.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleBend.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/BondStretch.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/BondStretch.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Contribs.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Contribs.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/DistanceConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/DistanceConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversion.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversion.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversions.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversions.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Nonbonded.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Nonbonded.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Params.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Params.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/PositionConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/PositionConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionAngle.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionAngle.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionConstraint.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/TorsionConstraint.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Utils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Utils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/AlignPoints.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/AlignPoints.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Conrec.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Conrec.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers/PowerEigenSolver.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers/PowerEigenSolver.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Matrix.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Matrix.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/BFGSOpt.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/BFGSOpt.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/SquareMatrix.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/SquareMatrix.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/SymmMatrix.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/SymmMatrix.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Numerics/Vector.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Numerics/Vector.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Grid3D.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Grid3D.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/GridUtils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/GridUtils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/point.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/point.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform2D.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform2D.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform3D.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform3D.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformGrid3D.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformGrid3D.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformRealValueGrid3D.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformRealValueGrid3D.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Geometry/Utils.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Geometry/Utils.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/Features/Feature.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/Features/Feature.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/ChemicalFeature.h...
Parsing file /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/ChemicalFeature.h...
Preprocessing /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/FreeChemicalFeature.h...
Parsing file /build/reproducible-path/rdkit-202409.6/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...
Searc/build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:62: warning: documented symbol 'for experimental torsion angle RDKit::DGeomHelpers::preferences' was not declared or defined.
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h:1187: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined.
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h:1203: warning: documented symbol 'modifies molecule in RDKit::MolOps::place' was not declared or defined.
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.h:90: warning: documented symbol 'enum RDKIT_MOLSTANDARDIZE_EXPORT RDKit::MolStandardize::PipelineStatus' was not declared or defined.
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:94: warning: no matching file member found for
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string RDKit::toJSON(const std::map &rgr, const std::string &prefix="")
Possible candidates:
'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRow &rgr, const std::string &prefix="")' at line 82 of file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h
'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRows &rgr, const std::string &prefix="")' at line 86 of file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h
'RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupColumn &rgr, const std::string &prefix="")' at line 90 of file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.h
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override'
hing 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 RealValueVect.h...
Generating code for file SparseBitVect.h...
Generating code for file SparseIntVect.h...
Generating code for file BoundsMatrix.h...
Generating code for file ChiralSet.h...
Generating code for file ChiralViolationContrib.h...
Generating code for file ChiralViolationContribs.h...
Generating code for file DistGeomUtils.h...
Generating code for file DistViolationContrib.h...
Generating code for file DistViolationContribs.h...
Generating code for file FourthDimContrib.h...
Generating code for file FourthDimContribs.h...
Generating code for file TriangleSmooth.h...
Generating code for file Feature.h...
Generating code for file AngleConstraints.h...
Generating code for file Contrib.h...
Generating code for file DistanceConstraints.h...
Generating code for file ForceField.h...
Generating code for file AngleBend.h...
Generating code for file AngleBend.h...
Generating code for file AngleConstraint.h...
Generating code for file AngleConstraint.h...
Generating code for file AngleConstraint.h...
Generating code for file BondStretch.h...
Generating code for file BondStretch.h...
Generating code for file Contribs.h...
Generating code for file Contribs.h...
Generating code for file DistanceConstraint.h...
Generating code for file DistanceConstraint.h...
Generating code for file DistanceConstraint.h...
Generating code for file Nonbonded.h...
Generating code for file Nonbonded.h...
Generating code for file OopBend.h...
Generating code for file Params.h...
Generating code for file Params.h...
Generating code for file PositionConstraint.h...
Generating code for file PositionConstraint.h...
Generating code for file PositionConstraint.h...
Generating code for file StretchBend.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 TorsionConstraint.h...
Generating code for file Inversion.h...
Generating code for file Inversions.h...
Generating code for file Utils.h...
Generating code for file Utils.h...
Generating code for file Grid3D.h...
Generating code for file GridUtils.h...
Generating code for file point.h...
Generating code for file Transform.h...
Generating code for file Transform2D.h...
Generating code for file Transform3D.h...
Generating code for file UniformGrid3D.h...
Generating code for file UniformRealValueGrid3D.h...
Generating code for file Abbreviations.h...
Generating code for file Atom.h...
Generating code for file atomic_data.h...
Generating code for file AtomIterators.h...
Generating code for file Atropisomers.h...
Generating code for file Bond.h...
Generating code for file BondIterators.h...
Generating code for file Canon.h...
Generating code for file CartesianProduct.h...
Generating code for file Enumerate.h...
Generating code for file EnumerateBase.h...
Generating code for file EnumerateTypes.h...
Generating code for file EnumerationPickler.h...
Generating code for file EnumerationStrategyBase.h...
Generating code for file EvenSamplePairs.h...
Generating code for file RandomSample.h...
Generating code for file RandomSampleAllBBs.h...
Generating code for file PreprocessRxn.h...
Generating code for file Reaction.h...
Generating code for file ReactionFingerprints.h...
Generating code for file ReactionParser.h...
Generating code for file ReactionPickler.h...
Generating code for file ReactionRunner.h...
Generating code for file ReactionUtils.h...
Generating code for file SanitizeRxn.h...
Generating code for file ChemTransforms.h...
Generating code for file MolFragmenter.h...
Generating code for file Chirality.h...
Generating code for file CIPLabeler.h...
Generating code for file CIPMol.h...
Generating code for file AtropisomerBond.h...
Generating code for file Configuration.h...
Generating code for file Sp2Bond.h...
Generating code for file Tetrahedral.h...
Generating code for file Descriptor.h...
Generating code for file Digraph.h...
Generating code for file Edge.h...
Generating code for file Mancude.h...
Generating code for file Node.h...
Generating code for file Priority.h...
Generating code for file Pairlist.h...
Generating code for file Rule1a.h...
Generating code for file Rule1b.h...
Generating code for file Rule2.h...
Generating code for file Rule3.h...
Generating code for file Rule4a.h...
Generating code for file Rule4b.h...
Generating code for file Rule4c.h...
Generating code for file Rule5.h...
Generating code for file Rule5New.h...
Generating code for file Rule6.h...
Generating code for file Rules.h...
Generating code for file SequenceRule.h...
Generating code for file Sort.h...
Generating code for file TooManyNodesException.h...
Generating code for file Conformer.h...
Generating code for file DepictUtils.h...
Generating code for file EmbeddedFrag.h...
Generating code for file RDDepictor.h...
Generating code for file Templates.h...
Generating code for file TemplateSmiles.h...
Generating code for file Deprotect.h...
Generating code for file AtomFeat.h...
Generating code for file AUTOCORR2D.h...
Generating code for file AUTOCORR3D.h...
Generating code for file BCUT.h...
Generating code for file ConnectivityDescriptors.h...
Generating code for file CoulombMat.h...
Generating code for file Crippen.h...
Generating code for file Data3Ddescriptors.h...
Generating code for file DCLV.h...
Generating code for file EEM.h...
Generating code for file GETAWAY.h...
Generating code for file Lipinski.h...
Generating code for file MolData3Ddescriptors.h...
Generating code for file MolDescriptors.h...
Generating code for file MolDescriptors3D.h...
Generating code for file MolSurf.h...
Generating code for file MORSE.h...
Generating code for file MQN.h...
Generating code for file OxidationNumbers.h...
Generating code for file PBF.h...
Generating code for file PMI.h...
Generating code for file Property.h...
Generating code for file RDF.h...
Generating code for file RegisterDescriptor.h...
Generating code for file USRDescriptor.h...
Generating code for file WHIM.h...
Generating code for file 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 FileWriters.h...
Generating code for file GeneralFileReader.h...
Generating code for file MaestroProperties.h...
Generating code for file MolFileStereochem.h...
Generating code for file MolSGroupParsing.h...
Generating code for file MolSGroupWriting.h...
Generating code for file MolSupplier.h...
Generating code for file MolSupplier.v1API.h...
Generating code for file MolWriters.h...
Generating code for file MultithreadedMolSupplier.h...
Generating code for file MultithreadedSDMolSupplier.h...
Generating code for file MultithreadedSmilesMolSupplier.h...
Generating code for file PNGParser.h...
Generating code for file ProximityBonds.h...
Generating code for file SequenceParsers.h...
Generating code for file SequenceWriters.h...
Generating code for file FilterCatalog.h...
Generating code for file FilterCatalogEntry.h...
Generating code for file FilterMatcherBase.h...
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G/build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistGeomUtils.h:93: warning: The following parameter of DistGeom::constructForceField(const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets, double weightChiral=1.0, double weightFourthDim=0.1, std::map< std::pair< int, int >, double > *extraWeights=nullptr, double basinSizeTol=5.0, boost::dynamic_bitset<> *fixedPts=nullptr) is not documented:
parameter 'fixedPts'
/build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContribs.h:46: warning: argument 'cset' of command @param is not found in the argument list of DistGeom::ChiralViolationContribs::ChiralViolationContribs(ForceFields::ForceField *owner)
/build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContribs.h:46: warning: argument 'weight' of command @param is not found in the argument list of DistGeom::ChiralViolationContribs::ChiralViolationContribs(ForceFields::ForceField *owner)
/build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContribs.h:36: warning: argument 'idx' of command @param is not found in the argument list of DistGeom::FourthDimContribs::FourthDimContribs(ForceFields::ForceField *owner)
/build/reproducible-path/rdkit-202409.6/Code/DistGeom/FourthDimContribs.h:36: warning: argument 'weight' of command @param is not found in the argument list of DistGeom::FourthDimContribs::FourthDimContribs(ForceFields::ForceField *owner)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h:24: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h:24: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.h:24: warning: The following parameters of ForceFields::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented:
parameter 'minAngleDeg'
parameter 'maxAngleDeg'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:65: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:65: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:65: warning: The following parameters of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented:
parameter 'minAngleDeg'
parameter 'maxAngleDeg'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:53: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:53: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.h:53: warning: The following parameters of ForceFields::AngleConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented:
parameter 'minAngleDeg'
parameter 'maxAngleDeg'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h:61: warning: argument 'forceConst' of command @param is not found in the argument list of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, bool relative, double minLen, double maxLen, double forceConstant)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h:61: warning: The following parameter of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, bool relative, double minLen, double maxLen, double forceConstant) is not documented:
parameter 'forceConstant'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h:50: warning: argument 'forceConst' of command @param is not found in the argument list of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, double minLen, double maxLen, double forceConstant)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.h:50: warning: The following parameter of ForceFields::DistanceConstraintContribs::addContrib(unsigned int idx1, unsigned int idx2, double minLen, double maxLen, double forceConstant) is not documented:
parameter 'forceConstant'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.h:159: warning: argument 'snapshotFreq' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.h:159: warning: argument 'snapshotVect' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.h:144: warning: The following parameters of ForceFields::ForceField::minimize(unsigned int snapshotFreq, RDKit::SnapshotVect *snapshotVect, unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) are not documented:
parameter 'snapshotFreq'
parameter 'snapshotVect'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/PositionConstraint.h:25: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleBend.h:31: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/AngleBend.h:31: warning: The following parameters of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) are not documented:
parameter 'mmffAngleParams'
parameter 'mmffPropParamsCentralAtom'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'bondType' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end1Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end2Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.h:28: warning: The following parameter of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) is not documented:
parameter 'mmffBondParams'
/build/reproducible-path/rdkit-202409.6/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 compound ChemicalFeatures::FreeChemicalFeature...
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Gener/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.h:32: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.h:32: warning: The following parameters of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) are not documented:
parameter 'mmffStbnParams'
parameter 'mmffAngleParams'
parameter 'mmffBondParams1'
parameter 'mmffBondParams2'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionAngle.h:31: warning: argument 'torsionType' of command @param is not found in the argument list of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams)
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/TorsionAngle.h:31: warning: The following parameter of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) is not documented:
parameter 'mmffTorParams'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Nonbonded.h:30: warning: The following parameter of ForceFields::MMFF::VdWContrib::VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants) is not documented:
parameter 'mmffVdWConstants'
/build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversion.h:27: warning: The following parameter of ForceFields::UFF::InversionContrib::InversionContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, int at2AtomicNum, bool isCBoundToO, double oobForceScalingFactor=1.0) is not documented:
parameter 'oobForceScalingFactor'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/RDDepictor.h:392: warning: argument 'refPattern' of command @param is not found in the argument list of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/RDDepictor.h:392: 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'
ating docs for compound ForceFields::MMFF::MMFFVdWCollection...
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Generating docs for compound RDInfoThe/build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstanceGroup.h:276: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented:
parameter 'mol'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: argument 'seq' of command @param is not found in the argument list of RDKit::HELMToMol(const char *helm, bool sanitize=true)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: The following parameter of RDKit::HELMToMol(const char *helm, bool sanitize=true) is not documented:
parameter 'helm'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.h:69: warning: The following parameter of RDKit::LayeredFingerprintMol(const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool branchedPaths=true, const std::vector< std::uint32_t > *fromAtoms=nullptr) is not documented:
parameter 'fromAtoms'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.h:232: warning: argument 'doRandom' of command @param is not found in the argument list of RDKit::MolFragmentToSmiles(const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:36: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:36: warning: The following parameter of RDKit::MolToMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:111: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:111: warning: The following parameter of RDKit::MolToMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.h:180: warning: The following parameters of RDKit::MolToMrvBlock(const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) are not documented:
parameter 'mol'
parameter 'includeStereo'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.h:155: warning: The following parameters of RDKit::MolToMrvFile(const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool prettyPrint=false) are not documented:
parameter 'mol'
parameter 'fName'
parameter 'includeStereo'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:227: warning: argument 'fName' of command @param is not found in the argument list of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:227: warning: The following parameter of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) is not documented:
parameter 'fname'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:97: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV2KMolBlock(const ROMol &mol, const MolWriterParams ¶ms=MolWriterParams(), int confId=-1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:97: warning: The following parameter of RDKit::MolToV2KMolBlock(const ROMol &mol, const MolWriterParams ¶ms=MolWriterParams(), int confId=-1) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:66: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV3KMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:66: warning: The following parameter of RDKit::MolToV3KMolBlock(const ROMol &mol, const MolWriterParams ¶ms, int confId=-1) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:142: warning: argument 'MolWriterParams' of command @param is not found in the argument list of RDKit::MolToV3KMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileWriters.h:142: warning: The following parameter of RDKit::MolToV3KMolFile(const ROMol &mol, const std::string &fName, const MolWriterParams ¶ms, int confId=-1) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.h:120: warning: The following parameter of RDKit::PatternFingerprintMol(const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false) is not documented:
parameter 'tautomericFingerprint'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: argument 'useBondOrders' of command @param is not found in the argument list of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: The following parameters of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) are not documented:
parameter 'useBondOrder'
parameter 'bitInfo'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionRunner.h:94: warning: The following parameter of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) is not documented:
parameter 'product'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/ChemTransforms.h:114: warning: argument 'useChirality' of command @param is not found in the argument list of RDKit::replaceCore(const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: argument 'reactantTemplateIdx' of command @param is not found in the argument list of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: The following parameters of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) are not documented:
parameter 'rxn'
parameter 'reactantIdx'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:84: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:84: warning: The following parameter of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:97: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:97: warning: The following parameter of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.h:152: warning: The following parameter of RDKit::SubstructMatch(T1 &mol, const T2 &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000, int numThreads=1) is not documented:
parameter 'numThreads'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::AtomEnvironment::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const=0 are not documented:
parameter 'AdditionalOutput'
parameter 'fpSize'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Reaction.h:219: warning: argument 'maxProducts' of command @param is not found in the argument list of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Reaction.h:219: warning: The following parameter of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const is not documented:
parameter 'numProducts'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h:430: warning: argument 'matches' of command @param is not found in the argument list of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented:
parameter 'matchVect'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 is not documented:
parameter 'matchVect'
ory::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::ControlCHandler...
Generating docs for compound RDKit::CustomPropHandler...
Generating docs for compound RDKit::CXXAtomIterator...
Generating docs for nested compound RDKit::CXXAtomIterator::CXXAtomIter...
Generating docs for compound RDKit::CXXBondIterator...
Generating docs for nested compound RDKit::CXXBondIterator::CXXBondIter...
Generating docs for compound RDKit::DataStructsExplicitBitVecPropHandler...
Generating docs for compound RDKit::Dict...
Generating docs for nested compound RDKit::Dict::Pair...
Generating docs for compound RDKit::DiscreteDistMat...
Generating docs for compound RDKit::DiscreteValueVect...
Generating docs for compound RDKit::DrawColour...
Generating docs for compound RDKit::EnumerateLibrary...
Generating docs for compound RDKit::EnumerateLibraryBase...
Generating docs for compound RDKit::EnumerationParams...
Generating docs for compound RDKit::EnumerationStrategyBase...
Generating docs for compound RDKit::EnumerationStrategyException...
Generating docs for compound RDKit::EvenSamplePairsStrategy...
Generating docs for compound RDKit::ExclusionList...
Generating docs for compound RDKit::FeatureFileParseException...
Generating docs for compound RDKit::FileParseException...
Generating docs for compound RDKit::FilterCatalog...
Generating docs for compound RDKit::FilterCatalogEntry...
Generating docs for compound RDKit::FilterCatalogParams...
Generating docs for compound RDKit::FilterData_t...
Generating docs for compound RDKit::FilterHierarchyMatcher...
Generating docs for compound RDKit::FilterMatch...
Generating docs for compound RDKit::FilterMatcherBase...
Generating docs for compound RDKit::FilterProperty_t...
Generating docs for compound RDKit::FingerprintArguments...
Generating docs for compound RDKit::FingerprintFuncArguments...
Generating docs for compound RDKit::FingerprintGenerator...
Generating docs for compound RDKit::FingerprintVarianceScoreData...
Generating docs for compound RDKit::FixedMolSizeMolBundle...
Generating docs for compound RDKit::FPBReader...
Generating docs for compound RDKit::FPHolderBase...
Generating docs for compound RDKit::FragCatalogEntry...
Generating docs for compound RDKit::FragCatGenerator...
Generating docs for compound RDKit::FragCatParams...
Generating docs for compound RD/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecule has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: The following parameter of RDKit::MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1) is not documented:
parameter 'highlight_bonds'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_atom_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_bond_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'confId' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.h:149: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecules has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/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'
Kit::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 >...
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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...
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Generating docs for compound RDKit::MarvinPlus...
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Generating docs for compound RDKit::MarvinSruCoModSgroup...
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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...
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Generating docs for compound RDKit::MolBundle...
Generating docs for compound RDKit::MolCatalogEntry...
Generating docs for compound RDKit::MolCatalogParams...
Generating docs for compound RDKit::MolChemicalFeature...
Generating docs for compound RDKit::MolChemicalFeatureDef...
Generating docs for compound RDKit::MolChemicalFeatureFactory...
Generating docs for compound RDKit::MolDraw2D...
Generating docs for compound RDKit::MolDraw2DCairo...
Generating docs for compound RDKit::MolDraw2DJS...
Generating docs for compound RDKit::MolDraw2DQt...
Generating docs for compound RDKit::MolDraw2DSVG...
Generating docs for compound RDKit::MolDraw2Dwx...
Generating docs for compound RDKit::MolDrawOptions...
Generating docs for compound RDKit::MolHolder...
Generating docs for compound RDKit::MolHolderBase...
Generating docs for compound RDKit::MolMatchFinalCheckFunctor...
Generating docs for compound RDKit::MolPickler...
Generating docs for compound RDKit::MolPicklerException...
Generating docs for compound RDKit::MolSanitizeException...
Generating docs for compound RDKit::MolWriter...
Generating docs for compound RDKit::MolWriterParams...
Generating docs for compound RDKit::MolzipParams...
Generating docs for compound RDKit::MrvWriterParams...
Generating docs for compound RDKit::MultiFPBReader...
Generating docs for compound RDKit::PairHolder...
Generating docs for compound RDKit::PatternHolder...
Generating docs for compound RDKit::PDBWriter...
Generating docs for compound RDKit::PeriodicTable...
Generating docs for compound RDKit::QueryAtom...
Generating docs for compound RDKit::QueryAtomIterator_...
Generating docs for compound RDKit::QueryBond...
Generating docs for compound RDKit::RandomSampleAllBBsStrategy...
Generating docs for c/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Resonance.h:114: warning: argument 'numThreads' of command @param is not found in the argument list of RDKit::ResonanceMolSupplier::ResonanceMolSupplier(ROMol &mol, unsigned int flags=0, unsigned int maxStructs=1000)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h:336: warning: argument 'matches' of command @param is not found in the argument list of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented:
parameter 'matchVect'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Abbreviations.h:104: warning: The following parameter of RDKit::Abbreviations::findApplicableAbbreviationMatches(const ROMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4) is not documented:
parameter 'mol'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::AtomPair::AtomPairAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented:
parameter 'AdditionalOutput'
parameter 'fpSize'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairs.h:97: warning: The following parameter of RDKit::AtomPairs::getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false, bool use2D=true, int confId=-1) is not documented:
parameter 'confId'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.h:75: warning: The following parameter of RDKit::AtomPairs::getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false) is not documented:
parameter 'includeChirality'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Canon.h:98: warning: The following parameters of RDKit::Canon::canonicalizeFragment(ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, const std::vector< unsigned int > &ranks, MolStack &molStack, const boost::dynamic_bitset<> *bondsInPlay=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=false, bool doRandom=false, bool doChiralInversions=true) are not documented:
parameter 'bondsInPlay'
parameter 'bondSymbols'
parameter 'doIsomericSmiles'
parameter 'doRandom'
parameter 'doChiralInversions'
ompound 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::RealValueVect...
Generating docs for compound RDKit::RecursiveStructureQuery...
Generating docs for compound RDKit::ResonanceMolSupplier...
Generating docs for compound RDKit::ResonanceMolSupplierCallback...
Generating docs for compound RDKit::RGroupData...
Generating docs for compound RDKit::RGroupDecompData...
Generating docs for nested compound RDKit::RGroupDecompData::UsedLabels...
Generating docs for compound RDKit::RGroupDecomposition...
Generating docs for compound RDKit::RGroupDecompositionChromosome...
Generating docs for compound RDKit::RGroupDecompositionParameters...
Generating docs for compound RDKit::RGroupDecompositionProcessResult...
Generating docs for compound RDKit::RGroupGa...
Generating docs for compound RDKit::RGroupMatch...
Generating docs for compound RDKit::RGroupScorer...
Generating docs for compound RDKit::RigorousEnhancedStereoException...
Generating docs for compound RDKit::RingInfo...
Generating docs for compound RDKit::ROMol...
Generating docs for compound RDKit::RWMol...
Generating docs for compound RDKit::RxnSanitizeException...
Generating docs for compound RDKit::SDWriter...
Generating docs for compound RDKit::SLNParseException...
Generating docs for compound RDKit::SmartsMatcher...
Generating docs for compound RDKit::SmilesWriteParams...
Generating docs for compound RDKit::SmilesWriter...
Generating docs for compound RDKit::Snapshot...
Generating docs for compound RDKit::SparseIntVect...
Generating docs for compound RDKit::StereoBondThresholds...
Generating docs for compound RDKit::StereoGroup...
Generating docs for compound RDKit::SubstanceGroup...
Generating docs for nested compound RDKit::SubstanceGroup::AttachPoint...
Generating docs for nested compound RDKit::SubstanceGroup::CState...
Generating docs for compound RDKit::SubstanceGroupException...
Generating docs for compound RDKit::SubstructLibrary...
Generating docs for compound RDKit::SubstructMatchParameters...
Generating docs for compound RDKit::TautomerPatternHolder...
Generating docs for compound RDKit::TautomerQuery...
Generating docs for compound RDKit::TDTWriter...
Generating docs for compound RDKit::Trajectory...
Generating docs for compound RDKit::UnimplementedFPException...
Generating docs for compound RDKit::UsedLabelMap...
Generating docs for compound RDKit::VarianceDataForLabel...
Generating docs for namespace RDKit::Abbreviations
Generating docs for compound RDKit::Abbreviations::AbbreviationDefinition...
Generating docs for compound RDKit::Abbreviations::AbbreviationMatch...
Generating docs for namespace RDKit::Abbreviations::common_properties
Generating docs for namespace RDKit::Abbreviations::Utils
Generating docs for namespace RDKit::AtomPair
Generating docs for compound RDKit::AtomPair::AtomPairArguments...
Generating docs for compound RDKit::AtomPair::AtomPairAtomEnv...
Generating docs for compound RDKit::AtomPair::AtomPairAtomInvGenerator...
Generating docs for compound RDKit::AtomPair::AtomPairEnvGenerator...
Generating docs for namespace RDKit::AtomPairs
Generating docs for namespace RDKit::Atropisomers
Generating docs for namespace RDKit::Canon
Generating docs for compound RDKit::Canon::AtomCompareFunctor...
Generating docs for compound RDKit::Canon::bondholder...
Generating docs for compound RDKit::Canon::canon_atom...
Generating docs for compound RDKit::Canon::ChiralAtomCompareFunctor...
Generating docs for compound RDKit::Canon::MolStackElem...
Generating docs for compound RDKit::Canon::MolStackUnion...
Generating docs for compound RDKit::Canon::SpecialChiralityAtomCompareFunctor...
Generating docs for compound RDKit::Canon::SpecialSymmetryAtomCompareFunctor...
Generat/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.h:414: warning: The following parameters of RDKit::Chirality::findMesoCenters(const ROMol &mol, bool includeIsotopes=true, bool includeAtomMaps=false) are not documented:
parameter 'includeIsotopes'
parameter 'includeAtomMaps'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.h:143: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented:
parameter 'flagPossible'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.h:195: warning: The following parameter of RDKit::Chirality::getTrigonalBipyramidalAxialBond(const Atom *center, int which=0) is not documented:
parameter 'center'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPLabeler.h:44: warning: The following parameter of RDKit::CIPLabeler::assignCIPLabels(ROMol &mol, unsigned int maxRecursiveIterations=0) is not documented:
parameter 'maxRecursiveIterations'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Lipinski.h:45: warning: argument 'strict' of command @param is not found in the argument list of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Lipinski.h:45: warning: The following parameter of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) is not documented:
parameter 'useStrictDefinition'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/USRDescriptor.h:68: warning: The following parameter of RDKit::Descriptors::USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int > > &atomIds, int confId=-1) is not documented:
parameter 'atomIds'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.h:328: warning: The following parameter of RDKit::DGeomHelpers::EmbedMultipleConfs(ROMol &mol, INT_VECT &res, unsigned int numConfs=10, int numThreads=1, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=true, bool useMacrocycle14config=true, unsigned int timeout=0) is not documented:
parameter 'timeout'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:37: warning: The following parameter of RDKit::DGeomHelpers::setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds=true, bool scaleVDW=false, bool useMacrocycle14config=false, bool forceTransAmides=true) is not documented:
parameter 'forceTransAmides'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h:98: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented:
parameter 'matchVect'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h:218: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented:
parameter 'matchVect'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.h:161: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 98 in file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:98: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented:
parameter 'matchVect'
ing docs for namespace RDKit::Canon::detail
Generating docs for namespace RDKit::Chirality
Generating docs for compound RDKit::Chirality::BondWedgingParameters...
Generating docs for compound RDKit::Chirality::StereoInfo...
Generating docs for compound RDKit::Chirality::WedgeInfoAtropisomer...
Generating docs for compound RDKit::Chirality::WedgeInfoBase...
Generating docs for compound RDKit::Chirality::WedgeInfoChiral...
Generating docs for namespace RDKit::Chirality::detail
Generating docs for namespace RDKit::CIPLabeler
Generating docs for compound RDKit::CIPLabeler::AtropisomerBond...
Generating docs for compound RDKit::CIPLabeler::CIPMol...
Generating docs for compound RDKit::CIPLabeler::CIPMolSpan...
Generating docs for nested compound RDKit::CIPLabeler::CIPMolSpan::CIPMolIter...
Generating docs for compound RDKit::CIPLabeler::Configuration...
Generating docs for compound RDKit::CIPLabeler::Digraph...
Generating docs for compound RDKit::CIPLabeler::Edge...
Generating docs for compound RDKit::CIPLabeler::MaxIterationsExceeded...
Generating docs for compound RDKit::CIPLabeler::Node...
Generating docs for compound RDKit::CIPLabeler::PairList...
Generating docs for compound RDKit::CIPLabeler::Priority...
Generating docs for compound RDKit::CIPLabeler::Rule1a...
Generating docs for compound RDKit::CIPLabeler::Rule1b...
Generating docs for compound RDKit::CIPLabeler::Rule2...
Generating docs for compound RDKit::CIPLabeler::Rule3...
Generating docs for compound RDKit::CIPLabeler::Rule4a...
Generating docs for compound RDKit::CIPLabeler::Rule4b...
Generating docs for compound RDKit::CIPLabeler::Rule4c...
Generating docs for compound RDKit::CIPLabeler::Rule5...
Generating docs for compound RDKit::CIPLabeler::Rule5New...
Generating docs for compound RDKit::CIPLabeler::Rule6...
Generating docs for compound RDKit::CIPLabeler::Rules...
Generating docs for compound RDKit::CIPLabeler::SequenceRule...
Generating docs for compound RDKit::CIPLabeler::Sort...
Generating docs for compound RDKit::CIPLabeler::Sp2Bond...
Generating docs for compound RDKit::CIPLabeler::Tetrahedral...
Generating docs for compound RDKit::CIPLabeler::TooManyNodesException...
Generating docs for namespace RDKit::CIPLabeler_detail
Generating docs for namespace RDKit::common_properties
Generating docs for namespace RDKit::constants
Generating docs for namespace RDKit::Deprotect
Generating docs for compound RDKit::Deprotect::DeprotectData...
Generating docs for namespace RDKit::Descriptors
Generating docs for compound RDKit::Descriptors::CrippenParamCollection...
Generating docs for compound RDKit::Descriptors::CrippenParams...
Generating docs for compound RDKit::Descriptors::DoubleCubicLatticeVolume...
Generating docs for compound RDKit::Descriptors::Properties...
Generating docs for compound RDKit::Descriptors::PropertyFunctor...
Generating docs for namespace RDKit::Descriptors::detail
Generating docs for namespace RDKit::detail
Generating docs for compound RDKit::detail::MCSParametersInternal...
Generating docs for namespace RDKit::details
Generating docs for namespace RDKit::DGeomHelpers
Generating docs for compound RDKit::DGeomHelpers::EmbedParameters...
Generating docs for namespace RDKit::DTags
Generating docs for namespace RDKit::EnumerationStrategyPickler
Generating docs for namespace RDKit::EnumerationTypes
Generating docs for namespace RDKit::FileParsers
Generating docs for namespace RDKit::FileParsers::schrodinger
Generating docs for namespace RDKit::FileParserUtils
Generating docs for namespace RDKit::FilterMatchOps
Generating docs for compound RDKit::FilterMatchOps::And...
Generating docs for compound RDKit::FilterMatchOps::Not...
Generating docs for compound RDKit::FilterMatchOps::Or...
Generating docs for namespace RDKit::FMCS
Generating docs for compound RDKit::FMCS::Composition2N...
Generating docs for compound RDKit::FMCS::DuplicatedSeedCache...
Generating docs for nested compound RDKit::FMCS::DuplicatedSeedCache::TKey...
Generating docs for compound RDKit::FMCS::ExecStatistics...
Generating docs for compound RDKit::FMCS::Graph...
Generating do/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.h:93: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::CreateShingling(const ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented:
parameter 'mol'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.h:132: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::Encode(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented:
parameter 'mol'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.h:183: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::EncodeSECFP(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1, size_t length=2048) is not documented:
parameter 'mol'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.h:28: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int maxCuts=3, unsigned int maxCutBonds=20, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented:
parameter 'pattern'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.h:49: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented:
parameter 'pattern'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h:149: warning: argument 'trans' of command @param is not found in the argument list of RDKit::MolAlign::getBestRMS(ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr, int numThreads=1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: The following parameters of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) are not documented:
parameter 'bondColours'
parameter 'highlight_radii'
parameter 'includeAnnotations'
parameter 'isReactionMol'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented:
parameter 'highlight_radii'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h:24: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.h:24: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented:
parameter 'highlight_radii'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:36: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCHLasso::DrawMolMCHLasso(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:36: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCHLasso::DrawMolMCHLasso(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented:
parameter 'highlight_radii'
cs 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::MMPA::detail
Generating docs for namespace RDKit::MolAlign
Generating docs for compound RDKit::MolAlign::LAP...
Generating docs for compound RDKit::MolAlign::MolAlignException...
Generating docs for compound RDKit::MolAlign::MolHistogram...
Generating docs for compound RDKit::MolAlign::O3A...
Generating docs for compound RDKit::MolAlign::O3AConstraint...
Generating docs for compound RDKit::MolAlign::O3AConstraintVect...
Generating docs for compound RDKit::MolAlign::O3AFuncData...
Generating docs for compound RDKit::MolAlign::SDM...
Generating docs for namespace RDKit::MolAlign::details
Generating docs for namespace RDKit::MolDraw2D_detail
Generating docs for compound RDKit::MolDraw2D_detail::AtomSymbol...
Generating docs for compound RDKit::MolDraw2D_detail::DrawAnnotation...
Generating docs for compound RDKit::MolDraw2D_detail::DrawMol...
Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCH...
Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine...
Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCHLasso...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShape...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArc...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArrow...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeDashedWedge...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeEllipse...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShapePolyLine...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSimpleLine...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSolidWedge...
Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeWavyLine...
Generating docs for compound RDKit::MolDraw2D_detail::DrawText...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextCairo...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFT...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTCairo...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTJS...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTQt...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTSV/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:263: warning: The following parameter of RDKit::MolEnumerator::enumerate(const ROMol &mol, size_t maxPerOperation=0) is not documented:
parameter 'mol'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:142: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:132: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:139: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:135: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:87: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:77: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:84: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:80: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:216: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:206: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:213: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.h:209: warning: Found unknown command '\override'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/MolInterchange.h:81: warning: The following parameter of RDKit::MolInterchange::MolsToJSONData(const std::vector< T > &mols, const JSONWriteParameters ¶ms=defaultJSONWriteParameters) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/MolInterchange.h:90: warning: The following parameter of RDKit::MolInterchange::MolToJSONData(const T &mol, const JSONWriteParameters ¶ms=defaultJSONWriteParameters) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.h:330: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) are not documented:
parameter 'mergeUnmappedOnly'
parameter 'mergeIsotopes'
G...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextJS...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextNotFT...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextQt...
Generating docs for compound RDKit::MolDraw2D_detail::DrawTextSVG...
Generating docs for compound RDKit::MolDraw2D_detail::LinePair...
Generating docs for compound RDKit::MolDraw2D_detail::StringRect...
Generating docs for namespace RDKit::MolDraw2DUtils
Generating docs for compound RDKit::MolDraw2DUtils::ContourParams...
Generating docs for namespace RDKit::MolEnumerator
Generating docs for compound RDKit::MolEnumerator::LinkNode...
Generating docs for compound RDKit::MolEnumerator::LinkNodeOp...
Generating docs for compound RDKit::MolEnumerator::MolEnumeratorOp...
Generating docs for compound RDKit::MolEnumerator::MolEnumeratorParams...
Generating docs for compound RDKit::MolEnumerator::PositionVariationOp...
Generating docs for compound RDKit::MolEnumerator::RepeatUnitOp...
Generating docs for namespace RDKit::MolEnumerator::detail
Generating docs for namespace RDKit::MolEnumerator::utils
Generating docs for namespace RDKit::MolFragmenter
Generating docs for compound RDKit::MolFragmenter::FragmenterBondType...
Generating docs for namespace RDKit::MolHash
Generating docs for namespace RDKit::MolInterchange
Generating docs for compound RDKit::MolInterchange::JSONParseParameters...
Generating docs for compound RDKit::MolInterchange::JSONWriteParameters...
Generating docs for namespace RDKit::MolOps
Generating docs for compound RDKit::MolOps::AdjustQueryParameters...
Generating docs for compound RDKit::MolOps::Hybridizations...
Generating docs for compound RDKit::MolOps::RemoveHsParameters...
Generating docs for namespace RDKit::MolOps::details
Generating docs for namespace RDKit::MolProcessing
Generating docs for namespace RDKit::MolProcessing::details
Generating docs for namespace RDKit::MolShapes
Generating docs for namespace RDKit::MolStandardize
Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogEntry...
Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogParams...
Generating docs for compound RDKit::MolStandardize::AllowedAtomsValidation...
Generating docs for compound RDKit::MolStandardize::ChargeCorrection...
Generating docs for compound RDKit::MolStandardize::CleanupParameters...
Generating docs for compound RDKit::MolStandardize::CompositeValidation...
Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation...
Generating docs for compound RDKit::MolStandardize::DisallowedRadicalValidation...
Generating docs for compound RDKit::MolStandardize::FeaturesValidation...
Generating docs for compound RDKit::MolStandardize::FragmentCatalogEntry...
Generating docs for compound RDKit::MolStandardize::FragmentCatalogParams...
Generating docs for compound RDKit::MolStandardize::FragmentRemover...
Generating docs for compound RDKit::MolStandardize::FragmentValidation...
Generating docs for compound RDKit::MolStandardize::Is2DValidation...
Generating docs for compound RDKit::MolStandardize::IsotopeValidation...
Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser...
Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest...
Generating docs for compound RDKit::MolStandardize::Layout2DValidation...
Generating docs for compound RDKit::MolStandardize::MetalDisconnector...
Generating docs for compound RDKit::MolStandardize::MetalDisconnectorOptions...
Generating docs for compound RDKit::MolStandardize::MolVSValidation...
Generating docs for compound RDKit::MolStandardize::NeutralValidation...
Generating docs for compound RDKit::MolStandardize::NoAtomValidation...
Generating docs for compound RDKit::MolStandardize::Normalizer...
Generating docs for compound RDKit::MolStandardize::Pipeline...
Generating docs for compound RDKit::MolStandardize::PipelineLogEntry...
Generating docs for compound RDKit::MolStandardize::PipelineOptions...
Generating docs for compound RDKit::MolStandardize::PipelineResult...
Generating docs /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:208: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.h:273: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::MorganFingerprint::MorganAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented:
parameter 'AdditionalOutput'
parameter 'fpSize'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.h:117: warning: The following parameter of RDKit::MorganFingerprints::getHashedFingerprint(const ROMol &mol, unsigned int radius, unsigned int nBits=2048, std::vector< boost::uint32_t > *invariants=nullptr, const std::vector< boost::uint32_t > *fromAtoms=nullptr, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=nullptr, bool includeRedundantEnvironments=false) is not documented:
parameter 'nBits'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, bool hashResults=false, const std::uint64_t fpSize=0) const are not documented:
parameter 'AdditionalOutput'
parameter 'fpSize'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:26: warning: The following parameter of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<> > *atomTypes=nullptr) is not documented:
parameter 'atomTypes'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.h:104: warning: argument 'bondIn' of command @param is not found in the argument list of RDKit::SmilesWrite::GetAtomSmiles(const Atom *atom, bool doKekule=false, const Bond *=nullptr, bool allHsExplicit=false, bool isomericSmiles=true)
for compound RDKit::MolStandardize::RDKitValidation...
Generating docs for compound RDKit::MolStandardize::Reionizer...
Generating docs for compound RDKit::MolStandardize::StereoValidation...
Generating docs for compound RDKit::MolStandardize::Tautomer...
Generating docs for compound RDKit::MolStandardize::TautomerCatalogEntry...
Generating docs for compound RDKit::MolStandardize::TautomerCatalogParams...
Generating docs for compound RDKit::MolStandardize::TautomerEnumerator...
Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorCallback...
Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorResult...
Generating docs for nested compound RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator...
Generating docs for compound RDKit::MolStandardize::TautomerTransform...
Generating docs for compound RDKit::MolStandardize::TransformCatalogEntry...
Generating docs for compound RDKit::MolStandardize::TransformCatalogParams...
Generating docs for compound RDKit::MolStandardize::Uncharger...
Generating docs for compound RDKit::MolStandardize::ValidationMethod...
Generating docs for namespace RDKit::MolStandardize::defaults
Generating docs for namespace RDKit::MolStandardize::Operations
Generating docs for namespace RDKit::MolStandardize::TautomerScoringFunctions
Generating docs for compound RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm...
Generating docs for namespace RDKit::MorganFingerprint
Generating docs for compound RDKit::MorganFingerprint::MorganArguments...
Generating docs for compound RDKit::MorganFingerprint::MorganAtomEnv...
Generating docs for compound RDKit::MorganFingerprint::MorganAtomInvGenerator...
Generating docs for compound RDKit::MorganFingerprint::MorganBondInvGenerator...
Generating docs for compound RDKit::MorganFingerprint::MorganEnvGenerator...
Generating docs for compound RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator...
Generating docs for namespace RDKit::MorganFingerprints
Generating docs for compound RDKit::MorganFingerprints::ss_matcher...
Generating docs for namespace RDKit::PicklerOps
Generating docs for namespace RDKit::PNGData
Generating docs for namespace RDKit::QueryOps
Generating docs for namespace RDKit::RascalMCES
Generating docs for compound RDKit::RascalMCES::PartitionSet...
Generating docs for compound RDKit::RascalMCES::RascalClusterOptions...
Generating docs for compound RDKit::RascalMCES::RascalOptions...
Generating docs for compound RDKit::RascalMCES::RascalResult...
Generating docs for namespace RDKit::RascalMCES::details
Generating docs for compound RDKit::RascalMCES::details::ClusNode...
Generating docs for namespace RDKit::RDKitFP
Generating docs for compound RDKit::RDKitFP::RDKitFPArguments...
Generating docs for compound RDKit::RDKitFP::RDKitFPAtomEnv...
Generating docs for compound RDKit::RDKitFP::RDKitFPAtomInvGenerator...
Generating docs for compound RDKit::RDKitFP::RDKitFPEnvGenerator...
Generating docs for namespace RDKit::RDKitFPUtils
Generating docs for namespace RDKit::RDTypeTag
Generating docs for namespace RDKit::RDTypeTag::detail
Generating docs for compound RDKit::RDTypeTag::detail::Value...
Generating docs for namespace RDKit::ReactionRunnerUtils
Generating docs for namespace RDKit::ReducedGraphs
Generating docs for namespace RDKit::RxnOps
Generating docs for namespace RDKit::ScaffoldNetwork
Generating docs for compound RDKit::ScaffoldNetwork::NetworkEdge...
Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetwork...
Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetworkParams...
Generating docs for namespace RDKit::ScaffoldNetwork::detail
Generating docs for namespace RDKit::SGroupParsing
Generating docs for namespace RDKit::SGroupWriting
Generating docs for namespace RDKit::SLNParse
Generating docs for compound RDKit::SLNParse::AttribType...
Generating docs for namespace RDKit::SmartsWrite
Generating docs for namespace RDKit::SmilesParse
Generating docs for compound RDKit::SmilesParse::SmilesParseException...
Generating docs for namespace RDKit::SmilesWrite
Generating /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:94: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool includeChirality=false, uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=true, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:94: warning: The following parameter of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool includeChirality=false, uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, bool countSimulation=true, std::uint32_t fpSize=2048, std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, bool ownsAtomInvGen=false) is not documented:
parameter 'countSimulation'
/build/reproducible-path/rdkit-202409.6/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=false, const uint32_t torsionAtomCount=4, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:32: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality=false, const uint32_t torsionAtomCount=4, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048) is not documented:
parameter 'countSimulation'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:68: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::TopologicalTorsionAtomEnv(OutputType bitId, INT_VECT atomPath) is not documented:
parameter 'atomPath'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.h:123: warning: The following parameters of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(FingerprintArguments *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented:
parameter 'AdditionalOutput'
parameter 'fpSize'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h:95: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::v1::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h:95: warning: The following parameter of RDKit::v1::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) is not documented:
parameter 'filename'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/FileParsers.h:76: warning: argument 'line' from the argument list of RDKit::v1::MolDataStreamToMol has multiple @param documentation sections
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h:46: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::v2::CDXMLParser::MolsFromCDXMLFile(const std::string &filename, const CDXMLParserParams ¶ms=CDXMLParserParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.h:46: warning: The following parameter of RDKit::v2::CDXMLParser::MolsFromCDXMLFile(const std::string &filename, const CDXMLParserParams ¶ms=CDXMLParserParams()) is not documented:
parameter 'filename'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'removeHs' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: argument 'strictParsing' of command @param is not found in the argument list of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:176: warning: The following parameter of RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier(const std::string &fileName, const MolFileParserParams ¶ms=MolFileParserParams()) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'delimiter' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'smilesColumn' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'nameColumn' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'titleLine' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:261: warning: The following parameter of RDKit::v2::FileParsers::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName, const SmilesMolSupplierParams ¶ms=SmilesMolSupplierParams()) is not documented:
parameter 'params'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'nameRecord' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'confId2D' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'confId3D' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams())
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSupplier.h:353: warning: The following parameter of RDKit::v2::FileParsers::TDTMolSupplier::TDTMolSupplier(const std::string &fileName, const TDTMolSupplierParams ¶ms=TDTMolSupplierParams()) is not documented:
parameter 'params'
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...
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Generating docs for namespace RD/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:117: warning: argument 'pos' of command @param is not found in the argument list of RDMIF::Coulomb::Coulomb(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:117: warning: The following parameter of RDMIF::Coulomb::Coulomb(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0) is not documented:
parameter 'positions'
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:220: warning: argument 'pos' of command @param is not found in the argument list of RDMIF::CoulombDielectric::CoulombDielectric(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0, double epsilon=80.0, double xi=4.0)
/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.h:220: warning: The following parameter of RDMIF::CoulombDielectric::CoulombDielectric(const std::vector< double > &charges, const std::vector< RDGeom::Point3D > &positions, double probeCharge=1.0, bool absVal=false, double alpha=0.0, double cutoff=1.0, double epsilon=80.0, double xi=4.0) is not documented:
parameter 'positions'
/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/HierarchicalClusterPicker.h:48: warning: The following parameter of RDPickers::HierarchicalClusterPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize) const is not documented:
parameter 'distMat'
/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const
/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const
/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/LeaderPicker.h:87: warning: The following parameters of RDPickers::LeaderPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize, const RDKit::INT_VECT &firstPicks, double threshold, int nthreads) const are not documented:
parameter 'threshold'
parameter 'nthreads'
/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const
/build/reproducible-path/rdkit-202409.6/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
Kit::v2::ReactionParser
Generating docs for namespace RDKit::v2::SmilesParse
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Running plantuml with JAVA...
type lookup cache used 36956/65536 hits=217530 misses=41055
symbol lookup cache used 32486/65536 hits=291606 misses=32486
finished...
(cd /build/reproducible-path/rdkit-202409.6/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202409.6 /usr/bin/make html)
make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/Docs/Book'
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Running Sphinx v8.1.3
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reading sources... [ 95%] source/rdkit.VLib.NodeLib.SmilesDupeFilter
reading sources... [ 96%] source/rdkit.VLib.NodeLib.SmilesOutput
reading sources... [ 96%] source/rdkit.VLib.NodeLib.SmilesSupply
reading sources... [ 97%] source/rdkit.VLib.Output
reading sources... [ 97%] source/rdkit.VLib.Supply
reading sources... [ 97%] source/rdkit.VLib.Transform
reading sources... [ 98%] source/rdkit.rdBase
reading sources... [ 98%] source/rdkit.utils
reading sources... [ 98%] 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-202409.6/Docs/Book/BackwardsIncompatibleChanges.md:49: WARNING: duplicate label changes to canonicalization, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/BackwardsIncompatibleChanges.md [autosectionlabel.BackwardsIncompatibleChanges]
/build/reproducible-path/rdkit-202409.6/Docs/Book/Cartridge.md:732: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/BackwardsIncompatibleChanges.md [autosectionlabel.Cartridge]
/build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst:7: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cartridge.md [autosectionlabel.Cookbook]
/build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst:10: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cartridge.md [autosectionlabel.Cookbook]
/build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst:2581: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cartridge.md [autosectionlabel.Cookbook]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md:3: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst [autosectionlabel.GettingStartedInC++]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md:305: WARNING: duplicate label writing molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst [autosectionlabel.GettingStartedInC++]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:12: WARNING: duplicate label what is this?, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:30: WARNING: duplicate label reading single molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:104: WARNING: duplicate label reading sets of molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:208: WARNING: duplicate label writing molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:393: WARNING: duplicate label writing sets of molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:434: WARNING: duplicate label working with molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:438: WARNING: duplicate label looping over atoms and bonds, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:481: WARNING: duplicate label ring information, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:550: WARNING: duplicate label modifying molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:618: WARNING: duplicate label working with 2d molecules: generating depictions, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:668: WARNING: duplicate label working with 3d molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:794: WARNING: duplicate label preserving molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:850: WARNING: duplicate label drawing molecules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:1089: WARNING: duplicate label substructure searching, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:1154: WARNING: duplicate label stereochemistry in substructure matches, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:1192: WARNING: duplicate label atom map indices in smarts, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:3434: WARNING: duplicate label the sssr problem, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInC++.md [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst:3848: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst [autosectionlabel.GettingStartedInPython]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:424: WARNING: duplicate label building rdkit for development, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:430: WARNING: duplicate label where should i put my code?, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:434: WARNING: duplicate label coding standards, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:447: WARNING: duplicate label tests, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing]
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:481: WARNING: duplicate label documentation, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md [autosectionlabel.GettingStartedWithContributing]
/build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md:430: WARNING: duplicate label recommended extras, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md [autosectionlabel.Install]
/build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md:474: WARNING: duplicate label testing the build (optional, but recommended), other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md [autosectionlabel.Install]
/build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md:479: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst [autosectionlabel.Install]
/build/reproducible-path/rdkit-202409.6/Docs/Book/Overview.md:107: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Install.md [autosectionlabel.Overview]
/build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:179: WARNING: duplicate label aromaticity, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst [autosectionlabel.RDKit_Book]
/build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:385: WARNING: duplicate label dative bonds, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst [autosectionlabel.RDKit_Book]
/build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:575: WARNING: duplicate label stereochemistry, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst [autosectionlabel.RDKit_Book]
/build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:1304: WARNING: duplicate label chemical features, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst [autosectionlabel.RDKit_Book]
/build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:2504: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Cookbook.rst [autosectionlabel.RDKit_Book]
/build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:2602: WARNING: duplicate label rdkit fingerprints, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedInPython.rst [autosectionlabel.RDKit_Book]
/build/reproducible-path/rdkit-202409.6/Docs/Book/RDKit_Book.rst:2768: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/Overview.md [autosectionlabel.RDKit_Book]
WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Avalon]
WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.rst [autosectionlabel.source/rdkit.Chem]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst:115: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Avalon.rst [autosectionlabel.source/rdkit.Chem]
WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs]
WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw]
WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState]
WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps]
WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features]
WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle]
WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb]
WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey]
WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolStandardize.rst:6: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.MolStandardize]
WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolStandardize.rst [autosectionlabel.source/rdkit.Chem.Pharm2D]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D]
WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds]
WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum]
WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape]
WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers]
WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs]
WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdShapeAlign' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdSynthonSpaceSearch' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.DataManip]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip]
WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip.Metric]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.DataManip.Metric]
WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs]
WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst:17: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase]
WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry]
WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.ForceField]
WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.Geometry]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst [autosectionlabel.source/rdkit.Geometry]
WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.ML]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:18: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:26: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML]
WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster]
WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data]
WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors]
WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory]
WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils]
WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT]
WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring]
WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics]
WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters]
WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.VLib]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib]
WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib]
WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils]
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dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 375 warnings.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
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WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.Chem.AtomPairs]
WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.AtomPairs.rst [autosectionlabel.source/rdkit.Chem.ChemUtils]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.ChemUtils.rst [autosectionlabel.source/rdkit.Chem.Draw]
WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Draw.rst [autosectionlabel.source/rdkit.Chem.EState]
WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.EState.rst [autosectionlabel.source/rdkit.Chem.FeatMaps]
WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.FeatMaps.rst [autosectionlabel.source/rdkit.Chem.Features]
WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Features.rst [autosectionlabel.source/rdkit.Chem.Fingerprints]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fingerprints.rst [autosectionlabel.source/rdkit.Chem.Fraggle]
WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Fraggle.rst [autosectionlabel.source/rdkit.Chem.MolDb]
WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolDb.rst [autosectionlabel.source/rdkit.Chem.MolKey]
WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.MolKey.rst [autosectionlabel.source/rdkit.Chem.Pharm2D]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm2D.rst [autosectionlabel.source/rdkit.Chem.Pharm3D]
WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Pharm3D.rst [autosectionlabel.source/rdkit.Chem.Scaffolds]
WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Scaffolds.rst [autosectionlabel.source/rdkit.Chem.SimpleEnum]
WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.SpacialScore' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.SimpleEnum.rst [autosectionlabel.source/rdkit.Chem.Subshape]
WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Subshape.rst [autosectionlabel.source/rdkit.Chem.Suppliers]
WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.Suppliers.rst [autosectionlabel.source/rdkit.Chem.fmcs]
WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdDetermineBonds' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdShapeAlign' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdSynthonSpaceSearch' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.rst [autosectionlabel.source/rdkit.DataManip]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip]
WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Chem.fmcs.rst [autosectionlabel.source/rdkit.DataManip.Metric]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.DataManip.Metric]
WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.Metric.rst [autosectionlabel.source/rdkit.DataStructs]
WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst:17: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataStructs.rst [autosectionlabel.source/rdkit.Dbase]
WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Dbase.rst [autosectionlabel.source/rdkit.DistanceGeometry]
WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.ForceField]
WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DistanceGeometry.rst [autosectionlabel.source/rdkit.Geometry]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ForceField.rst [autosectionlabel.source/rdkit.Geometry]
WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.DataManip.rst [autosectionlabel.source/rdkit.ML]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:18: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst:26: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Geometry.rst [autosectionlabel.source/rdkit.ML]
WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.ML.Cluster]
WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Cluster.rst [autosectionlabel.source/rdkit.ML.Data]
WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Data.rst [autosectionlabel.source/rdkit.ML.Descriptors]
WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Descriptors.rst [autosectionlabel.source/rdkit.ML.InfoTheory]
WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.InfoTheory.rst [autosectionlabel.source/rdkit.ML.MLUtils]
WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.MLUtils.rst [autosectionlabel.source/rdkit.ML.SLT]
WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.SLT.rst [autosectionlabel.source/rdkit.ML.Scoring]
WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.Scoring.rst [autosectionlabel.source/rdkit.Numerics]
WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.Numerics.rst [autosectionlabel.source/rdkit.SimDivFilters]
WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.ML.rst [autosectionlabel.source/rdkit.VLib]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.SimDivFilters.rst [autosectionlabel.source/rdkit.VLib]
WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.rst [autosectionlabel.source/rdkit.VLib.NodeLib]
WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils]
/build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202409.6/Docs/Book/source/rdkit.VLib.NodeLib.rst [autosectionlabel.source/rdkit.utils]
WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised:
No module named 'rdkit' [autodoc.import_object]
looking for now-outdated files... none found
pickling environment... done
checking consistency... /build/reproducible-path/rdkit-202409.6/Docs/Book/data/README.md: WARNING: document isn't included in any toctree
done
preparing documents... done
copying assets...
copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/Makefile
Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/latexmkjarc
Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/latexmkrc
Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/make.bat
done
copying assets: done
processing RDKit.tex...
index
Overview
Install
GettingStartedInPython
RDKit_Book
GettingStartedWithContributing
Cookbook
Cartridge
BackwardsIncompatibleChanges
api-docs
source/rdkit
source/rdkit.Avalon
source/rdkit.Avalon.pyAvalonTools
source/rdkit.Chem
source/rdkit.Chem.AtomPairs
source/rdkit.Chem.AtomPairs.Pairs
source/rdkit.Chem.AtomPairs.Sheridan
source/rdkit.Chem.AtomPairs.Torsions
source/rdkit.Chem.AtomPairs.Utils
source/rdkit.Chem.ChemUtils
source/rdkit.Chem.ChemUtils.AlignDepict
source/rdkit.Chem.ChemUtils.BulkTester
source/rdkit.Chem.ChemUtils.DescriptorUtilities
source/rdkit.Chem.ChemUtils.SDFToCSV
source/rdkit.Chem.ChemUtils.TemplateExpand
source/rdkit.Chem.Draw
source/rdkit.Chem.Draw.IPythonConsole
source/rdkit.Chem.Draw.MolDrawing
source/rdkit.Chem.Draw.SimilarityMaps
source/rdkit.Chem.Draw.rdMolDraw2D
source/rdkit.Chem.Draw.rdMolDraw2DQt
source/rdkit.Chem.EState
source/rdkit.Chem.EState.AtomTypes
source/rdkit.Chem.EState.EState
source/rdkit.Chem.EState.EState_VSA
source/rdkit.Chem.EState.Fingerprinter
source/rdkit.Chem.FeatMaps
source/rdkit.Chem.FeatMaps.FeatMapParser
source/rdkit.Chem.FeatMaps.FeatMapPoint
source/rdkit.Chem.FeatMaps.FeatMapUtils
source/rdkit.Chem.FeatMaps.FeatMaps
source/rdkit.Chem.Features
source/rdkit.Chem.Features.FeatDirUtilsRD
source/rdkit.Chem.Features.ShowFeats
source/rdkit.Chem.Fingerprints
source/rdkit.Chem.Fingerprints.ClusterMols
source/rdkit.Chem.Fingerprints.DbFpSupplier
source/rdkit.Chem.Fingerprints.FingerprintMols
source/rdkit.Chem.Fingerprints.MolSimilarity
source/rdkit.Chem.Fingerprints.SimilarityScreener
source/rdkit.Chem.Fraggle
source/rdkit.Chem.Fraggle.FraggleSim
source/rdkit.Chem.MolDb
source/rdkit.Chem.MolDb.FingerprintUtils
source/rdkit.Chem.MolDb.Loader
source/rdkit.Chem.MolDb.Loader_orig
source/rdkit.Chem.MolDb.Loader_sa
source/rdkit.Chem.MolKey
source/rdkit.Chem.MolKey.InchiInfo
source/rdkit.Chem.MolKey.MolKey
source/rdkit.Chem.Pharm2D
source/rdkit.Chem.Pharm2D.Generate
source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D
source/rdkit.Chem.Pharm2D.Matcher
source/rdkit.Chem.Pharm2D.SigFactory
source/rdkit.Chem.Pharm2D.Utils
source/rdkit.Chem.Pharm3D
source/rdkit.Chem.Pharm3D.EmbedLib
source/rdkit.Chem.Pharm3D.ExcludedVolume
source/rdkit.Chem.Pharm3D.Pharmacophore
source/rdkit.Chem.Scaffolds
source/rdkit.Chem.Scaffolds.MurckoScaffold
source/rdkit.Chem.Scaffolds.rdScaffoldNetwork
source/rdkit.Chem.SimpleEnum
source/rdkit.Chem.SimpleEnum.Enumerator
source/rdkit.Chem.Subshape
source/rdkit.Chem.Subshape.BuilderUtils
source/rdkit.Chem.Subshape.SubshapeAligner
source/rdkit.Chem.Subshape.SubshapeBuilder
source/rdkit.Chem.Subshape.SubshapeObjects
source/rdkit.Chem.Suppliers
source/rdkit.Chem.Suppliers.DbMolSupplier
source/rdkit.Chem.Suppliers.MolSupplier
source/rdkit.Chem.fmcs
source/rdkit.Chem.fmcs.fmcs
source/rdkit.Chem.AllChem
source/rdkit.Chem.BRICS
source/rdkit.Chem.BuildFragmentCatalog
source/rdkit.Chem.ChemicalFeatures
source/rdkit.Chem.ChemicalForceFields
source/rdkit.Chem.Crippen
source/rdkit.Chem.Descriptors
source/rdkit.Chem.Descriptors3D
source/rdkit.Chem.EnumerateHeterocycles
source/rdkit.Chem.EnumerateStereoisomers
source/rdkit.Chem.FastSDMolSupplier
source/rdkit.Chem.FeatFinderCLI
source/rdkit.Chem.FilterCatalog
source/rdkit.Chem.FragmentCatalog
source/rdkit.Chem.FragmentMatcher
source/rdkit.Chem.Fragments
source/rdkit.Chem.FunctionalGroups
source/rdkit.Chem.GraphDescriptors
source/rdkit.Chem.Graphs
source/rdkit.Chem.Lipinski
source/rdkit.Chem.MACCSkeys
source/rdkit.Chem.MolCatalog
source/rdkit.Chem.MolStandardize
source/rdkit.Chem.MolStandardize.rdMolStandardize
source/rdkit.Chem.MolSurf
source/rdkit.Chem.PandasTools
source/rdkit.Chem.PeriodicTable
source/rdkit.Chem.PropertyMol
source/rdkit.Chem.PyMol
source/rdkit.Chem.QED
source/rdkit.Chem.Randomize
source/rdkit.Chem.Recap
source/rdkit.Chem.ReducedGraphs
source/rdkit.Chem.RegistrationHash
source/rdkit.Chem.SATIS
source/rdkit.Chem.SaltRemover
source/rdkit.Chem.ShowMols
source/rdkit.Chem.SpacialScore
source/rdkit.Chem.TemplateAlign
source/rdkit.Chem.TorsionFingerprints
source/rdkit.Chem.inchi
source/rdkit.Chem.rdchem
source/rdkit.Chem.rdDistGeom
source/rdkit.Chem.rdqueries
source/rdkit.Chem.rdFMCS
source/rdkit.Chem.rdMolAlign
source/rdkit.Chem.rdMolHash
source/rdkit.Chem.rdReducedGraphs
source/rdkit.Chem.rdtrajectory
source/rdkit.Chem.rdMolTransforms
source/rdkit.Chem.rdmolfiles
source/rdkit.Chem.rdPartialCharges
source/rdkit.Chem.rdMolCatalog
source/rdkit.Chem.rdCoordGen
source/rdkit.Chem.rdMolChemicalFeatures
source/rdkit.Chem.rdMMPA
source/rdkit.Chem.rdRGroupDecomposition
source/rdkit.Chem.rdForceFieldHelpers
source/rdkit.Chem.rdDepictor
source/rdkit.Chem.rdChemicalFeatures
source/rdkit.Chem.rdmolops
source/rdkit.Chem.rdFreeSASA
source/rdkit.Chem.rdMolInterchange
source/rdkit.Chem.rdShapeHelpers
source/rdkit.Chem.rdinchi
source/rdkit.Chem.rdChemReactions
source/rdkit.Chem.rdSubstructLibrary
source/rdkit.Chem.rdfiltercatalog
source/rdkit.Chem.rdfragcatalog
source/rdkit.Chem.rdMolDescriptors
source/rdkit.Chem.rdFingerprintGenerator
source/rdkit.Chem.rdMHFPFingerprint
source/rdkit.Chem.rdSLNParse
source/rdkit.Chem.rdAbbreviations
source/rdkit.Chem.rdDeprotect
source/rdkit.Chem.rdMolEnumerator
source/rdkit.Chem.rdCIPLabeler
source/rdkit.Chem.rdTautomerQuery
source/rdkit.Chem.rdEHTTools
source/rdkit.Chem.rdDetermineBonds
source/rdkit.Chem.rdShapeAlign
source/rdkit.Chem.rdSynthonSpaceSearch
source/rdkit.DataManip
source/rdkit.DataManip.Metric
source/rdkit.DataManip.Metric.rdMetricMatrixCalc
source/rdkit.DataStructs
source/rdkit.DataStructs.BitEnsemble
source/rdkit.DataStructs.BitEnsembleDb
source/rdkit.DataStructs.BitUtils
source/rdkit.DataStructs.LazySignature
source/rdkit.DataStructs.TopNContainer
source/rdkit.DataStructs.VectCollection
source/rdkit.DataStructs.cDataStructs
source/rdkit.Dbase
source/rdkit.Dbase.DbConnection
source/rdkit.Dbase.DbInfo
source/rdkit.Dbase.DbModule
source/rdkit.Dbase.DbResultSet
source/rdkit.Dbase.DbUtils
source/rdkit.Dbase.StorageUtils
source/rdkit.DistanceGeometry
source/rdkit.DistanceGeometry.DistGeom
source/rdkit.ForceField
source/rdkit.ForceField.rdForceField
source/rdkit.Geometry
source/rdkit.Geometry.rdGeometry
source/rdkit.ML
source/rdkit.ML.Cluster
source/rdkit.ML.Cluster.Butina
source/rdkit.ML.Cluster.ClusterUtils
source/rdkit.ML.Cluster.ClusterVis
source/rdkit.ML.Cluster.Clusters
source/rdkit.ML.Cluster.Murtagh
source/rdkit.ML.Cluster.Resemblance
source/rdkit.ML.Cluster.Standardize
source/rdkit.ML.Cluster.Clustering
source/rdkit.ML.Data
source/rdkit.ML.Data.DataUtils
source/rdkit.ML.Data.FindQuantBounds
source/rdkit.ML.Data.MLData
source/rdkit.ML.Data.Quantize
source/rdkit.ML.Data.cQuantize
source/rdkit.ML.Data.SplitData
source/rdkit.ML.Data.Stats
source/rdkit.ML.Data.Transforms
source/rdkit.ML.Descriptors
source/rdkit.ML.Descriptors.CompoundDescriptors
source/rdkit.ML.Descriptors.Descriptors
source/rdkit.ML.Descriptors.MoleculeDescriptors
source/rdkit.ML.Descriptors.Parser
source/rdkit.ML.InfoTheory
source/rdkit.ML.InfoTheory.BitClusterer
source/rdkit.ML.InfoTheory.BitRank
source/rdkit.ML.InfoTheory.entropy
source/rdkit.ML.InfoTheory.rdInfoTheory
source/rdkit.ML.MLUtils
source/rdkit.ML.MLUtils.VoteImg
source/rdkit.ML.SLT
source/rdkit.ML.SLT.Risk
source/rdkit.ML.Scoring
source/rdkit.ML.Scoring.Scoring
source/rdkit.ML.MatOps
source/rdkit.ML.files
source/rdkit.Numerics
source/rdkit.Numerics.rdAlignment
source/rdkit.SimDivFilters
source/rdkit.SimDivFilters.SimilarityPickers
source/rdkit.SimDivFilters.rdSimDivPickers
source/rdkit.VLib
source/rdkit.VLib.NodeLib
source/rdkit.VLib.NodeLib.DbMolSupply
source/rdkit.VLib.NodeLib.DbPickleSupplier
source/rdkit.VLib.NodeLib.SDSupply
source/rdkit.VLib.NodeLib.SmartsMolFilter
source/rdkit.VLib.NodeLib.SmartsRemover
source/rdkit.VLib.NodeLib.SmilesDupeFilter
source/rdkit.VLib.NodeLib.SmilesOutput
source/rdkit.VLib.NodeLib.SmilesSupply
source/rdkit.VLib.Filter
source/rdkit.VLib.Node
source/rdkit.VLib.Output
source/rdkit.VLib.Supply
source/rdkit.VLib.Transform
source/rdkit.utils
source/rdkit.utils.cactvs
source/rdkit.utils.chemutils
source/rdkit.utils.fileutils
source/rdkit.utils.listutils
source/rdkit.utils.spiral
source/rdkit.rdBase
source/rdkit.RDConfig
source/rdkit.RDLogger
source/rdkit.RDPaths
source/rdkit.RDRandom
source/rdkit.TestRunner
GettingStartedInC++
resolving references...
/build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:273: WARNING: 'myst' cross-reference target not found: 'building-rdkit-for-development' [myst.xref_missing]
WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError("<urllib3.connection.HTTPSConnection object at 0x7f31a1ff2510>: Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))]
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Chapter 1.
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[]\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN
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tstrap.sh [][]with[]libraries=python,
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[]\T1/qtm/m/n/10 You can en-able sup-port for gen-er-at-ing InChI strings and I
nChI keys by adding the ar-gu-ment
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[]\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at
e 2D de-pic-tions for molecules that
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[]\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu
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Chapter 4.
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Chapter 5.
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Chapter 6.
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Chapter 7.
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Chapter 1.
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[]\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN
-IME com-mu-nity site:
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Chapter 2.
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[]\T1/qtm/m/n/10 If you want to use the python wrap-pers: \T1/txtt/m/n/10 ./boo
tstrap.sh [][]with[]libraries=python,
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[]\T1/qtm/m/n/10 You can en-able sup-port for gen-er-at-ing InChI strings and I
nChI keys by adding the ar-gu-ment
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\T1/qtm/m/n/10 This sec-tion as-sumes that python is in-stalled in \T1/txtt/m/n
/10 C:[]Python36 that the boost libraries have been
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[]\T1/txtt/m/n/10 DBOOST_ROOT=C:/boost []DRDK_BUILD_INCHI_SUPPORT=ON []DRDK_BUI
LD_AVALON_SUPPORT=ON
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[]\T1/txtt/m/n/10 DRDK_BUILD_PGSQL=ON []DPostgreSQL_ROOT="C:[]Program Files[]Po
stgreSQL[]9.5" []G"Visual
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[]\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po
stgresql[]9.5" []D "C:[]
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[]\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po
stgresql[]9.5" []D "C:[]
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Chapter 3.
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[]\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at
e 2D de-pic-tions for molecules that
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\T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun
c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem.
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[]\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu
nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor.
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[]\T1/txtt/m/n/10 [cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:
4]1)[C:2](=[O:1])[N:13]=[N+:14]=[N-
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[]\T1/txtt/m/n/10 [$([O,S;H1;v2;!$(*[]*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;[]])
,$([N;v3;!$(N[]*=[O,N,
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[]\T1/txtt/m/n/10 [#7;+,$([N;H2&+0][$([C,a]);!$([C,a](=O))]),$([N;H1&+0]([$([C,
a]);!$([C,
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\T1/txtt/m/n/10 a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0&+0]([C;!$(C(=O))])([
C;!$(C(=O))])[C;!
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[]\T1/qtm/m/n/10 Acidic|
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Chapter 4.
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[]\T1/qtm/m/n/10 Hence, a sin-gle change to SMARTS in-ter-pre-ta-tion, for ex-p
res-sions of the form:
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[97 <./parastereo_2.png> <./parastereo_1.png> <./potential_stereo_double_bond1.
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[]\T1/qtm/m/n/10 The clas-sic ex-am-ple of this is cis-platin - \T1/txtt/m/n/10
Cl[Pt@SP1](Cl)(<[][NH3])<[][NH3] \T1/qtm/m/n/10 - vs trans-platin -
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\T1/qtm/m/n/10 Here's the rd-kitj-son rep-re-sen-ta-tion of the stereo groups f
rom the molecule
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[]\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si-
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[]\T1/qtm/m/n/10 _Re-ac-tion-De-
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[]\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup
plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.
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[]\T1/qtm/m/n/10 This be-hav-ior is en-abled by de-fault and can be turned on/o
ff with the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.
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\T1/qtm/m/n/10 tions \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.CreateAtomStringProp
ertyList()\T1/qtm/m/n/10 , \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.
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[]\T1/qhv/m/n/10 Mix-
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png> <./enhanced_stereo_and1_trans_base.png> <./enhanced_stereo_and1_trans_expa
nd.png> <./enhanced_stereo_or1_or2_base.png> <./enhanced_stereo_or1_cis_base.pn
g> <./enhanced_stereo_or1_trans_base.png> <./enhanced_stereo_abs_and_base.png>
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[]\T1/qtm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/txtt/m
/n/10 StereoGroup \T1/qtm/m/n/10 us-ing the func-tion \T1/txtt/m/n/10 rdkit.Che
m.
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> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>]
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[]\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1
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\T1/qtm/m/n/10 ceived from 3D co-or-di-nates. The de-fault value is \T1/txtt/m/
n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-ment vari-
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\T1/qtm/m/n/10 able \T1/txtt/m/n/10 RDK_ENABLE_NONTETRAHEDRAL_STEREO \T1/qtm/m/
n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked from
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\T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA
llowNontetrahedralChirality() \T1/qtm/m/n/10 /
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\T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n
/10 or from Python us-ing the func-tions
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[]\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx
tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per-
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\T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is
\T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-
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\T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION
\T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked
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\T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality:
:setUseLegacyStereoPerception() \T1/qtm/m/n/10 /
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Chapter 5.
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Chapter 6.
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[]\T1/txtt/m/n/10 CC(C)C(O)C1C(=O)NC(CC)C(=O)N(C)CC(=O)N(C)C(CC(C)C)C(=O)NC(C(C
)C)C(=O)N(C)C(CC(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)N(C)C(CC(C)C)C(=O)N(C)C(CC(C)C)C(
=O)N(C)C(C(C)C)C(=O)N1C[][]
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Chapter 7.
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Chapter 8.
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\T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl
,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl,
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\T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]],
[N,P](=O)[O[]],
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\T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[
]], S([O[]])[O[]], S(=O)([O[]])[O[]],
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Chapter 9.
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[236]
[237]
[238]
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[241]
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Chapter 10.
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\T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple,
an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an
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[]\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key
word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt
/m/n/10 returns the index of the
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Chapter 11.
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Chapter 12.
(./RDKit.ind)
[275] (./RDKit.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texmf/fonts/type1/public/tex-
gyre/qhvb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qhvbi.pfb></usr/sha
re/texmf/fonts/type1/public/tex-gyre/qhvr.pfb></usr/share/texmf/fonts/type1/pub
lic/tex-gyre/qtmb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmr.pfb></
usr/share/texmf/fonts/type1/public/tex-gyre/qtmri.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/txfonts
/tcxtt.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb>
Output written on RDKit.pdf (279 pages, 2962408 bytes).
Transcript written on RDKit.log.
Latexmk: Getting log file 'RDKit.log'
Latexmk: Examining 'RDKit.fls'
Latexmk: Examining 'RDKit.log'
Latexmk: Index file 'RDKit.idx' was written
Latexmk: Log file says output to 'RDKit.pdf'
Have index file 'RDKit.idx', RDKit.ind RDKit
Latexmk: All targets (RDKit.pdf) are up-to-date
make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex'
pdflatex finished; the PDF files are in _build/latex.
make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/Docs/Book'
make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6'
cp -r rdkit obj-*/
find /build/reproducible-path/rdkit-202409.6 -name rdchem.so
/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
PYTHONPATH=/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib:" dh_auto_test
cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42
make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j42
UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/DartConfiguration.tcl
Parse Config file:/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/DartConfiguration.tcl
Add coverage exclude regular expressions.
UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/DartConfiguration.tcl
Parse Config file:/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/DartConfiguration.tcl
Test project /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
Connected to MAKE jobserver
test 1
Start 1: testCoordGen
1: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/testCoordGen
1: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen
1: Test timeout computed to be: 1500
test 2
Start 2: pyCoordGen
2: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/External/CoordGen/Wrap/testCoordGen.py"
2: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/Wrap
2: Test timeout computed to be: 1500
test 3
Start 3: testDict
3: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral/testDict
3: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral
3: Test timeout computed to be: 1500
test 4
Start 4: testRDValue
4: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral/testRDValue
4: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral
4: Test timeout computed to be: 1500
test 5
Start 5: testConcurrentQueue
5: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral/testConcurrentQueue
5: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral
5: Test timeout computed to be: 1500
test 6
Start 6: dictTestsCatch
6: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral/dictTestsCatch
6: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral
6: Test timeout computed to be: 1500
test 7
Start 7: logTestsCatch
7: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral/logTestsCatch
7: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral
7: Test timeout computed to be: 1500
test 8
Start 8: testDataStructs
8: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/testDataStructs
8: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs
8: Test timeout computed to be: 1500
test 9
Start 9: testFPB
9: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/testFPB
9: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs
9: Test timeout computed to be: 1500
test 10
Start 10: testMultiFPB
10: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/testMultiFPB
10: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs
10: Test timeout computed to be: 1500
test 11
Start 11: catchDataStructs
11: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/catchDataStructs
11: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs
11: Test timeout computed to be: 1500
test 12
Start 12: pyBV
12: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testBV.py"
12: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap
12: Test timeout computed to be: 1500
test 13
Start 13: pyDiscreteValueVect
13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testDiscreteValueVect.py"
13: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap
13: Test timeout computed to be: 1500
test 14
Start 14: pyRealValueVect
14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testRealValueVect.py"
14: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap
14: Test timeout computed to be: 1500
test 15
Start 15: pySparseIntVect
15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testSparseIntVect.py"
15: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap
15: Test timeout computed to be: 1500
test 16
Start 16: pyFPB
16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testFPB.py"
16: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap
16: Test timeout computed to be: 1500
test 17
Start 17: testTransforms
17: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/testTransforms
17: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry
17: Test timeout computed to be: 1500
test 18
Start 18: testGrid
18: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/testGrid
18: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry
18: Test timeout computed to be: 1500
test 19
Start 19: testRealValueGrid
19: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/testRealValueGrid
19: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry
19: Test timeout computed to be: 1500
test 20
Start 20: geometryTestsCatch
20: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/geometryTestsCatch
20: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry
20: Test timeout computed to be: 1500
test 21
Start 21: testPyGeometry
21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/testGeometry.py"
21: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap
21: Test timeout computed to be: 1500
test 22
Start 22: testMatrices
22: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/testMatrices
22: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics
22: Test timeout computed to be: 1500
test 23
Start 23: testConrec
23: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/testConrec
23: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics
23: Test timeout computed to be: 1500
test 24
Start 24: testAlignment
24: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment
24: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment
24: Test timeout computed to be: 1500
test 25
Start 25: pyAlignment
25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/Wrap/testAlignment.py"
25: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap
25: Test timeout computed to be: 1500
test 26
Start 26: testOptimizer
26: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer
26: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer
26: Test timeout computed to be: 1500
test 27
Start 27: ForceFieldsCatch
27: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/ForceFieldsCatch
27: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField
27: Test timeout computed to be: 1500
test 28
Start 28: testUFFForceField
28: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField
28: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF
28: Test timeout computed to be: 1500
test 29
Start 29: testMMFFForceField
29: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField
29: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/MMFF
29: Test timeout computed to be: 1500
test 30
Start 30: pyForceFieldConstraints
30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap/testConstraints.py"
30: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/Wrap
30: Test timeout computed to be: 1500
test 31
Start 31: testDistGeom
31: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom
31: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom
31: Test timeout computed to be: 1500
test 32
Start 32: pyDistGeom
32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/rough_test.py"
32: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/Wrap
32: Test timeout computed to be: 1500
test 33
Start 33: graphmolTest1
33: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
33: Test timeout computed to be: 1500
test 34
Start 34: graphmolcpTest
34: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest
34: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
34: Test timeout computed to be: 1500
test 35
Start 35: graphmolqueryTest
35: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest
35: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
35: Test timeout computed to be: 1500
test 36
Start 36: graphmolMolOpsTest
36: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest
36: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
36: Test timeout computed to be: 1500
test 37
Start 37: graphmoltestChirality
37: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality
37: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
37: Test timeout computed to be: 1500
test 38
Start 38: graphmoltestPickler
38: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler
38: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
38: Test timeout computed to be: 1500
test 39
Start 39: graphmoltestPicklerGlobalSetting
39: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting
39: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
39: Test timeout computed to be: 1500
test 40
Start 40: graphmolIterTest
40: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest
40: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
40: Test timeout computed to be: 1500
test 41
Start 41: hanoiTest
41: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest
41: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
41: Test timeout computed to be: 1500
test 42
Start 42: graphmolMemTest1
42: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1
42: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
42: Test timeout computed to be: 1500
1: core
1: RDKit 2D
1:
1: 4 4 0 0 0 0 0 0 0 0999 V2000
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1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
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1: M END
1:
1: core+sidechain
1: RDKit 2D
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1: M END
1:
1: templated
1: RDKit 2D
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1:
1: core
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1:
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1: M END
1:
1: core+sidechain
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1:
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1:
1: templated
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1:
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1: core
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1:
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1:
1: core+sidechain
1: RDKit 2D
1:
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1: templated
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1: core+sidechain
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1: 2.2680 -1.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.4020 -2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.4021 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.5360 1.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.5360 2.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.8300 3.4295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.3300 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.3300 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.2812 -0.7457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.5900 -1.6966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.9208 -2.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.5682 -1.9046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.8686 0.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.2812 0.8725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 1 0
1: 3 4 1 0
1: 4 5 1 0
1: 2 6 1 0
1: 6 7 1 0
1: 7 8 1 0
1: 8 9 1 0
1: 9 10 1 0
1: 10 11 1 0
1: 7 12 1 0
1: 12 13 1 0
1: 13 14 1 0
1: 14 15 1 0
1: 15 16 1 0
1: 15 17 1 0
1: 14 18 1 0
1: 18 19 1 0
1: 13 1 1 0
1: 19 12 1 0
1: 11 9 1 0
1: M END
1:
1: core
1: RDKit 2D
1:
1: 5 4 0 0 0 0 0 0 0 0999 V2000
1: 1.2134 -0.4976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.3444 1.0006 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.5186 -0.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.3856 -0.0028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 1 0
1: 2 4 1 0
1: 4 5 1 0
1: M END
1:
1: core+sidechain
1: RDKit 2D
1:
1: 7 6 0 0 0 0 0 0 0 0999 V2000
1: -1.7333 -0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.8661 -0.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.8641 0.9303 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.0011 -0.5713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.8659 -0.0731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.8679 0.9269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.7309 -0.5749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 1 0
1: 2 4 1 0
1: 4 5 1 0
1: 5 6 1 0
1: 5 7 1 0
1: M END
1:
1: templated
1: RDKit 2D
1:
1: 7 6 0 0 0 0 0 0 0 0999 V2000
1: 1.2227 -0.4921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.3350 1.0058 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.5185 -0.5117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.3902 -0.0216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.2506 -0.5314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.4014 0.9784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 1 0
1: 2 4 1 0
1: 4 5 1 0
1: 5 6 1 0
1: 5 7 1 0
1: M END
1:
1: test1
1: RDKit 2D
1:
1: 12 12 0 0 0 0 0 0 0 0999 V2000
1: -0.2902 0.4155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.5740 0.9187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.4418 0.4219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.3060 0.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.3024 1.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.4454 -0.5781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.5812 -1.0813 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.2866 -0.5843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.1508 -1.0875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.0186 -0.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.0222 0.4095 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.8828 -1.0937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 2 0
1: 2 3 1 0
1: 3 4 1 0
1: 4 5 1 0
1: 3 6 2 0
1: 6 7 1 0
1: 7 8 2 0
1: 8 9 1 0
1: 9 10 1 0
1: 10 11 2 0
1: 10 12 1 0
1: 8 1 1 0
1: M END
1:
1: test2
1: RDKit 2D
1:
1: 5 4 0 0 0 0 0 0 0 0999 V2000
1: -0.4980 0.7210 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.0004 -0.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.8678 -0.6440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.5020 0.7182 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.8642 -0.6488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 1 0
1: 2 4 1 0
1: 2 5 1 0
1: M END
1:
3: [06:34:54] Testing Github940: property dictionaries leaking memory
3: [06:34:54] done
3: Testing RDValue
3: Testing RDAny
3: dict set int vect
3: dict get int vect
3: static boost any:0.000297 s
3: dynamic boost any:0.000929 s
3: static RDAny:0.000132 s
3: dynamic RDAny:0.00083 s
3: static RDValue:1e-06 s
3: dynamic RDValue:0.000161 s
3: deleted!
3: [06:34:54] -------------------------------------
3: [06:34:54] Testing String Pickle Roundtrips.
3: [06:34:54] done
3: [06:34:54] -------------------------------------
3: [06:34:54] Testing conversion of vect to string.
3: [06:34:54] done
3: [06:34:54] -------------------------------------
3: [06:34:54] Testing returning const references.
3: [06:34:54] any cast
3: [06:34:54] done: 0.000728 300000
3: [06:34:54] copy
3: [06:34:54] done: 0.000693 300000
3: [06:34:54] ref
3: [06:34:54] done: 0.00075 300000
3: [06:34:54] dict
3: [06:34:54] done: 0.001569 300000
3: [06:34:54] ref with hasVal
3: [06:34:54] done: 0.001322 300000
3: [06:34:54] done
3: [06:34:54] -------------------------------------
3: [06:34:54] Testing dict update.
3: [06:34:54] done
3: deleted!
3: deleted!
3: deleted!
3: deleted!
3: deleted!
3: deleted!
4: -- running tests --
4: min: -2147483648 -2147483648
4: min: 0 0
4: min: 2.22507e-308 2.22507e-308
4: min: 1.17549e-38 1.17549e-38
4: min: 0 0
4: == int
4: == double
4: == float
4: == unsigned int
4: == bool
4: == std::string
5: [06:34:54]
5: -----------------------------------------
5: [06:34:54] Finished: testPushAndPop()
5: [06:34:54]
5: -----------------------------------------
5: [06:34:54]
5: -----------------------------------------
6: Randomness seeded to: 676651126
6: ===============================================================================
6: All tests passed (32 assertions in 2 test cases)
6:
7: [06:34:54] should not be silent
7: [06:34:54] should not be silent
7: Randomness seeded to: 2733542274
7: [06:34:54] should not be silent
7: [06:34:54] should not be silent
7: [06:34:54] should not be silent
7: [06:34:54] should not be silent
7: [06:34:54] should not be silent
7: [06:34:54] should not be silent
7: [06:34:54] should not be silent
7: [06:34:54] should not be silent
7: ===============================================================================
7: All tests passed (26 assertions in 3 test cases)
7:
8: [06:34:54] pass
8: [06:34:54] v3 4
8: [06:34:54] v4 5
8: [06:34:54] SPARSE -----------------------------------
8: [06:34:54] Set 10: 0
8: [06:34:54] Set 11: 0
8: [06:34:54] Set 14: 0
8: [06:34:54] Set 10: 1
8: [06:34:54] Get 14: 1
8: [06:34:54] Num: 20
8: [06:34:54] NumOn: 3
8: [06:34:54] NumOff: 17
8: 10, 11, 14,
8: [06:34:54] t2[19]: 0
8: [06:34:54] t2[14]: 1
8: [06:34:54] t2[19]: 0
8: [06:34:54] t2[14]: 0
8: t1: 10, 11, 14,
8: t2: 10, 11, 15, 17,
8: t1|t2: 10, 11, 14, 15, 17,
8: t1&t2: 10, 11,
8: t1^t2: 14, 15, 17,
8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19,
8: except
8: [06:34:54] Explicit ----------------------------------
8: [06:34:54] Set 10: 0
8: [06:34:54] Set 11: 0
8: [06:34:54] Set 14: 0
8: [06:34:54] Set 10: 1
8: [06:34:54] Get 14: 1
8: [06:34:54] Num: 20
8: [06:34:54] NumOn: 3
8: [06:34:54] NumOff: 17
8: 10, 11, 14,
8: [06:34:54] t2[19]: 0
8: [06:34:54] t2[14]: 1
8: [06:34:54] t2[19]: 0
8: [06:34:54] t2[14]: 0
8: t1: 10, 11, 14,
8: t2: 10, 11, 15, 17,
8: t1|t2: 10, 11, 14, 15, 17,
8: t1&t2: 10, 11,
8: t1^t2: 14, 15, 17,
8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19,
8: except
8: [06:34:54] Done
8: [06:34:54] Test DiscreteValue Vectors 1 ----------------------------
8: [06:34:54] Expected failure: Value out of range
8: [06:34:54] Expected failure: Value out of range
8: [06:34:54] Expected failure: Value out of range
8: [06:34:54] Expected failure: Value out of range
8: [06:34:54] Expected failure: Value out of range
8: [06:34:54] Test DiscreteValue Vectors 2 ------------------------------
8: [06:34:54] Test DiscreteValue Vectors 3 ---------------------------
8: [06:34:54] Test DiscreteValue Operations -----------------------------
8: [06:34:54] Test DiscreteValue Operations 2 --------------------------
8: [06:34:54] Test SparseIntVect ------------------------------------
8: [06:34:54] Test SparseIntVect Serialization --------------------------
8: [06:34:54] Test BitVect Serialization -------------------------------
8: [06:34:54] Test BitVect to FPS -------------------------------
8: [06:34:54] Test BitVect to binary string -------------------------------
8: [06:34:54] Test Similarity Measures BitVect -------------------------------
8: [06:34:54] Test Similarity Measures SparseBitVect -------------------------------
8: [06:34:54] Test BitVect with all ones -------------------------------
8: [06:34:54] Test Explicit BitVects: Concatenation Operation -------------------------------
8: [06:34:54] Test bitmap operations -------------------------------
8: [06:34:54] Test bitmaps as properties -------------------------------
8: [06:34:54] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data-------------------------------
8: [06:34:54] Test RealValue Vectors 1: Constructors and Accessing Values -------------------------------
8: [06:34:54] Test RealValue Vectors 2: L1Norm -------------------------------
8: [06:34:54] Test RealValue Vectors 3: Pickles -------------------------------
8: [06:34:54] Test RealValue Vectors 4: Vector Operations -------------------------------
11: Randomness seeded to: 3711263348
11: ===============================================================================
11: All tests passed (3 assertions in 1 test case)
11:
17: ****************************************
17: testPointND
17: ****************************************
17: testPointOps3D
17: ****************************************
17: testPointOps2D
17: ****************************************
17: test12D
17: ref1: 1.95512 0.770032 ref2: 4.86164 3.34826
17: pt1: 0.946516 1.782 pt2: 2.86897 4.03808
17: ****************************************
17: test23D
17: ****************************************
17: test3MatMultiply
17: Pt1: 1 0 0 Pt2: 2 0 0
17: -Pt1: -1 -0 -0
17: tp1: 0 0 0 tp2: 0 0 0
17: tp1: 0 0 0 tp2: 0 0 0
17: tp1: 0 0 3 tp2: 0 0 3
17: npt1: 0 0 3 npt2: 0 0 4
17: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4
17: ****************************************
17: testFromQuaternion
17: ****************************************
18: ***********************************************************
18: Testing Grid
18: ---------------------------------
18: testUniformGrid1
18:
18: ---------------------------------
18: testUniformGrid2
18:
18: ---------------------------------
18: testUniformGridPickling
18:
18: ---------------------------------
18: testGridOps
18:
18: ---------------------------------
18: testUniformGridIndexing
18:
19: ***********************************************************
19: Testing RealValueGrid3D
19: ---------------------------------
19: test1UniformRealValueGrid3D
19:
19: ---------------------------------
19: test2UniformRealValueGrid3DPickling
19:
19: ---------------------------------
19: test3UniformRealValueGrid3DIndexing
19:
19: ---------------------------------
19: test4UniformRealValueGrid3DOps
19:
20: Randomness seeded to: 891950187
20: ===============================================================================
20: All tests passed (50 assertions in 5 test cases)
20:
22: [06:34:54] -----------------------------------------
22: [06:34:54] Testing RDNumerics: vectors and matrices Code
22: [06:34:54] ---------------------------------------
22: [06:34:54] test1Vector
22: [06:34:54] ---------------------------------------
22: [06:34:54] test2Matrix
22: [06:34:54] ---------------------------------------
22: [06:34:54] test3SquareMatrix
22: [06:34:54] ---------------------------------------
22: [06:34:54] test4SymmMatrix
24: -----------------------------------------
24: Testing Alignment Code
24: ---------------------------------------
24: testBasic
24: ---------------------------------------
24: testTriangle
24: ---------------------------------------
24: testFourPts
24: ---------------------------------------
24: testReflection
24: ---------------------------------------
26: -------------------------------------
26: Testing linear search.
26: done
26: -------------------------------------
26: Testing BFGS optimization.
26: done
1/235 Test #3: testDict ............................... Passed 0.08 sec
2/235 Test #4: testRDValue ............................ Passed 0.08 sec
3/235 Test #6: dictTestsCatch ......................... Passed 0.07 sec
4/235 Test #7: logTestsCatch .......................... Passed 0.07 sec
5/235 Test #8: testDataStructs ........................ Passed 0.07 sec
6/235 Test #9: testFPB ................................ Passed 0.07 sec
7/235 Test #10: testMultiFPB ........................... Passed 0.07 sec
8/235 Test #11: catchDataStructs ....................... Passed 0.07 sec
9/235 Test #17: testTransforms ......................... Passed 0.06 sec
10/235 Test #18: testGrid ............................... Passed 0.05 sec
11/235 Test #19: testRealValueGrid ...................... Passed 0.05 sec
12/235 Test #20: geometryTestsCatch ..................... Passed 0.05 sec
13/235 Test #22: testMatrices ........................... Passed 0.05 sec
14/235 Test #24: testAlignment .......................... Passed 0.04 sec
15/235 Test #26: testOptimizer .......................... Passed 0.04 sec
test 43
Start 43: resMolSupplierTest
43: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest
43: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
43: Test timeout computed to be: 1500
test 44
Start 44: molBundleTest
44: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest
44: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
44: Test timeout computed to be: 1500
test 45
Start 45: testSGroup
45: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup
45: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
45: Test timeout computed to be: 1500
test 46
Start 46: test-valgrind
46: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind
46: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
46: Test timeout computed to be: 1500
test 47
Start 47: graphmolTestsCatch
47: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
47: Test timeout computed to be: 1500
test 48
Start 48: graphmolOrganometallicsCatch
48: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch
48: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
48: Test timeout computed to be: 1500
test 49
Start 49: graphmolSGroupCatch
49: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch
49: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
49: Test timeout computed to be: 1500
test 50
Start 50: graphmolAdjustQueryCatch
50: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch
50: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
50: Test timeout computed to be: 1500
test 51
Start 51: chiralityTestsCatch
51: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch
51: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
51: Test timeout computed to be: 1500
test 52
Start 52: canonTestsCatch
52: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch
52: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
52: Test timeout computed to be: 1500
test 53
Start 53: moliteratorTestsCatch
53: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch
53: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
53: Test timeout computed to be: 1500
test 54
Start 54: queryTestsCatch
54: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch
54: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
54: Test timeout computed to be: 1500
test 55
Start 55: molbundleTestsCatch
55: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch
55: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
55: Test timeout computed to be: 1500
test 56
Start 56: pickleTestsCatch
56: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch
56: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
56: Test timeout computed to be: 1500
test 57
Start 57: tableTestsCatch
57: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/tableTestsCatch
57: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
57: Test timeout computed to be: 1500
28: -------------------------------------
28: Unit tests for force field basics.
28: done
28: -------------------------------------
28: Unit tests for basics of UFF bond-stretch terms.
28: done
28: -------------------------------------
28: Unit tests for UFF bond-stretch terms.
28: done
28: -------------------------------------
28: Unit tests for basics of UFF angle terms.
28: done
28: -------------------------------------
28: Unit tests for UFF angle-bend terms.
28: theta = 3.14159; theta0 = 3.14159
28: theta = 2.094395, param1.theta0 = 2.094395
28: done
28: -------------------------------------
28: Test Simple UFF molecule optimizations.
28: done
28: -------------------------------------
28: Unit tests for UFF nonbonded terms.
28: done
28: -------------------------------------
28: Test UFF torsional terms.
28: done
28: -------------------------------------
28: Test UFF Parameter objects
28: -------------------------------------
28: Test Simple UFF molecule optimization, part 2.
28: done
28: -------------------------------------
28: Test UFF Torsion Conflicts.
28: C 0.4783 -0.7477 -0.0753
28: C -0.5465 -0.0176 0.3519
28: C -0.5114 1.4472 0.0870
28: H -1.5201 -0.4838 0.2485
28: H 0.4696 1.8363 0.3367
28: O -1.2618 1.9423 0.6934
28: F -0.7163 1.6298 -0.9622
28: done
28: -------------------------------------
28: Unit tests for UFF distance constraint terms.
28: done
28: -------------------------------------
28: Unit tests for all UFF constraint terms.
28: done
28: -------------------------------------
28: Unit tests for copying UFF ForceFields.
28: done
28: -------------------------------------
28: Unit test for UFF butane scan.
23: Randomness seeded to: 3760147162
23: ===============================================================================
23: All tests passed (76 assertions in 3 test cases)
23:
16/235 Test #23: testConrec ............................. Passed 0.10 sec
27: Randomness seeded to: 2169208548
27: ===============================================================================
27: All tests passed (20 assertions in 2 test cases)
27:
17/235 Test #27: ForceFieldsCatch ....................... Passed 0.09 sec
29: -------------------------------------
29: Official MMFF validation suite.
31: ***********************************************************
31: test1
31: ***********************************************************
31: testIssue216
31: Rows: 4 Columns: 4
31: 0 1 1 1
31: 1 0 1 1
31: 1 1 0 1
31: 1 1 1 0
31: ***********************************************************
31:
18/235 Test #31: testDistGeom ........................... Passed 0.09 sec
33: Atoms:
33: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb:
33: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb:
33: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb:
33: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb:
33: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb:
33: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb:
33: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb:
33: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: arom?: 1 query: AtomAtomicNum
33: 8 22 Ti chg: 0 deg: 1 exp: N/A imp: N/A hyb:
33: Bonds:
33: 0 0->1 order: 1
33: 1 1->2 order: 2
33: 2 2->3 order: 1
33: 3 0->4 order: 1
33: 4 5->6 order: 3
33: 5 6->7 order: 1
33: 6 7->8 order: 2
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: bond already exists
33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp
33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second)
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
33: 3# 0x00005557E133704C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00005557E1331081 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 5# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 7# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: bond already exists
33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp
33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second)
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
33: 3# 0x00005557E1325312 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00005557E1331081 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 5# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 7# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: attempt to add self-bond
33: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp
33: Failed Expression: atomIdx1 != atomIdx2
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
33: 3# 0x00005557E13254F8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00005557E1331081 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 5# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 7# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: bond already exists
33: Violation occurred on line 419 in file ./Code/GraphMol/ROMol.cpp
33: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second)
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
33: 3# 0x00005557E1325535 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00005557E1331081 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 5# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 7# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: attempt to add self-bond
33: Violation occurred on line 417 in file ./Code/GraphMol/ROMol.cpp
33: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx()
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
33: 3# 0x00005557E1325668 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00005557E1331081 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 5# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 7# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54] Explicit valence for atom # 0 B, 4, is greater than permitted
33: [06:34:54] Explicit valence for atom # 0 B, 4, is greater than permitted
33: [06:34:54]
33:
33: ****
33: Post-condition Violation
33: Element 'Xx' not found
33: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h
33: Failed Expression: anum > -1
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 3# 0x00005557E1359987 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00005557E13424FD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 5# 0x00005557E1331090 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 6# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 8# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54] -------------------------------------
33: [06:34:54] Test github381: thread-safe initialization of the periodic table
33: [06:34:54] done
33: [06:34:54] -------------------------------------
33: [06:34:54] Test github1041: Segfault for atom with no owner (expect some warnings)
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: no owner
33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
33: Failed Expression: dp_mol
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# 0x00005557E134FB9B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 3# 0x00005557E13310BD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 6# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: no owner
33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h
33: Failed Expression: dp_mol
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# 0x00005557E13309BE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 3# 0x00005557E13310BD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 6# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54] done
33: [06:34:54] -------------------------------------
33: [06:34:54] Test github1041: Segfault for atom with no owner (expect some warnings)
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: no owner
33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
33: Failed Expression: dp_mol
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# 0x00005557E134FB9B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 3# 0x00005557E13310C2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 6# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54]
33:
33: ****
33: Pre-condition Violation
33: no owner
33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h
33: Failed Expression: dp_mol
33: ----------
33: Stacktrace:
33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
33: 2# 0x00005557E13309BE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 3# 0x00005557E13310C2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: 4# 0x00007F47CE033CA8 in /lib/x86_64-linux-gnu/libc.so.6
33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
33: 6# 0x00005557E1331121 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1
33: ----------
33: ****
33:
33: [06:34:54] done
33: [06:34:54] -------------------------------------
33: [06:34:54] Test github1453: RWMol.clear() should reset the numBonds count.
33: [06:34:54] done
33: [06:34:54] -------------------------------------
33: [06:34:54] Test range-based for loops.
33: [06:34:54] done
33: [06:34:54] -------------------------------------
33: [06:34:54] Test github1642: Atom index type is too low for big molecules.
34:
34:
34:
34: COPY
19/235 Test #34: graphmolcpTest ......................... Passed 0.10 sec
35: [06:34:54] ---------------------- Test1
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test2
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test3
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test4
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test5
35: [06:34:54] Done!
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test issue 2892580
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test github issue 53: query molecules not matching [R]
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test queries using qualifiers instead of ==
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test Github issue 165: radicals not used in atom-atom matching
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test extra atom queries
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test extra bond queries
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test num heteroatom neighbor queries
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test atom type queries
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Test Github #2471: dummy atom queries are flagged as complex
35: [06:34:54] Done!
35: [06:34:54] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery()
35: [06:34:54] Done!
20/235 Test #35: graphmolqueryTest ...................... Passed 0.10 sec
38: [06:34:54] -------------------------------------
38: [06:34:54] Testing String Pickle Roundtrips.
38: [06:34:54] done
38: [06:34:54] -------------------------------------
38: [06:34:54] Testing reading existing pickle file (v2).
test 58
Start 58: molopsTestsCatch
58: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch
58: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol
58: Test timeout computed to be: 1500
test 59
Start 59: smiTest1
59: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1
59: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse
59: Test timeout computed to be: 1500
test 60
Start 60: smiTest2
60: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2
60: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse
60: Test timeout computed to be: 1500
test 61
Start 61: cxsmilesTest
61: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest
61: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse
61: Test timeout computed to be: 1500
test 62
Start 62: smaTest1
62: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1
62: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse
62: Test timeout computed to be: 1500
36: 1 1 2
36: 1 1 1
36: 2 1 0.75
36: path: 2
36: [06:34:54] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored
36: [06:34:54] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored
36: [06:34:54] Explicit valence for atom # 0 B, 5, is greater than permitted
36: [06:34:54] Explicit valence for atom # 1 C, 5, is greater than permitted
36: [06:34:54] Explicit valence for atom # 1 C, 5, is greater than permitted
36: [06:34:54] Explicit valence for atom # 1 C, 5, is greater than permitted
36: [06:34:54] Explicit valence for atom # 1 Si, 7, is greater than permitted
39: [06:34:54] done
41: [06:34:54] Testing the hanoi sort
41: [06:34:54] populating vectors
37: --------------------------
37: --------------------------
37: C/C=C/C(C)Cl
37: [06:34:54] Conflicting single bond directions around double bond at index 2.
37: [06:34:54] BondStereo set to STEREONONE and single bond directions set to NONE.
37: [06:34:54] Conflicting single bond directions around double bond at index 4.
37: [06:34:54] BondStereo set to STEREONONE and single bond directions set to NONE.
37: [06:34:54] Conflicting single bond directions around double bond at index 15.
37: [06:34:54] BondStereo set to STEREONONE and single bond directions set to NONE.
37: [06:34:54] Conflicting single bond directions around double bond at index 2.
37: [06:34:54] BondStereo set to STEREONONE and single bond directions set to NONE.
37: [06:34:54] Conflicting single bond directions around double bond at index 1.
37: [06:34:54] BondStereo set to STEREONONE and single bond directions set to NONE.
37: --------------------------------------------------
1: cyclosporine a
1: RDKit 2D
1:
1: 85 85 0 0 0 0 0 0 0 0999 V2000
1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 3 2 1 1
1: 3 4 1 0
1: 4 5 2 0
1: 4 6 1 0
1: 6 7 1 0
1: 7 8 1 0
1: 8 9 2 0
1: 8 10 1 0
1: 10 11 1 0
1: 11 12 1 0
1: 12 13 2 0
1: 12 14 1 0
1: 14 15 1 0
1: 15 16 1 0
1: 16 17 2 0
1: 16 18 1 0
1: 18 19 1 0
1: 19 20 1 0
1: 20 21 2 0
1: 20 22 1 0
1: 22 23 1 0
1: 23 24 1 0
1: 24 25 2 0
1: 24 26 1 0
1: 26 27 1 0
1: 27 28 1 0
1: 28 29 2 0
1: 28 30 1 0
1: 30 31 1 0
1: 31 32 1 0
1: 32 33 2 0
1: 32 34 1 0
1: 34 35 1 0
1: 35 36 1 0
1: 36 37 2 0
1: 36 38 1 0
1: 38 39 1 0
1: 39 40 1 0
1: 40 41 2 0
1: 40 42 1 0
1: 43 42 1 6
1: 43 44 1 0
1: 44 45 2 0
1: 44 46 1 0
1: 43 47 1 0
1: 47 48 1 0
1: 48 49 1 6
1: 48 50 1 0
1: 50 51 1 0
1: 51 52 2 0
1: 52 53 1 0
1: 47 54 1 1
1: 42 55 1 0
1: 39 56 1 6
1: 56 57 1 0
1: 56 58 1 0
1: 38 59 1 0
1: 35 60 1 6
1: 60 61 1 0
1: 61 62 1 0
1: 61 63 1 0
1: 34 64 1 0
1: 31 65 1 6
1: 65 66 1 0
1: 66 67 1 0
1: 66 68 1 0
1: 30 69 1 0
1: 27 70 1 6
1: 23 71 1 6
1: 19 72 1 6
1: 72 73 1 0
1: 73 74 1 0
1: 73 75 1 0
1: 18 76 1 0
1: 15 77 1 6
1: 77 78 1 0
1: 77 79 1 0
1: 11 80 1 6
1: 80 81 1 0
1: 81 82 1 0
1: 81 83 1 0
1: 10 84 1 0
1: 6 85 1 0
1: 46 3 1 0
1: M END
1:
1: single-double
1: RDKit 2D
1:
1: 17 16 0 0 0 0 0 0 0 0999 V2000
1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 1 0
1: 3 4 1 0
1: 4 5 1 0
1: 5 6 2 3
1: 6 7 1 0
1: 7 8 1 0
1: 8 9 1 0
1: 9 10 1 0
1: 10 11 2 3
1: 11 12 1 0
1: 12 13 2 3
1: 13 14 1 0
1: 14 15 2 3
1: 15 16 1 0
1: 16 17 1 0
1: M END
1:
1: cis-trans
1: RDKit 2D
1:
1: 10 9 0 0 0 0 0 0 0 0999 V2000
1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 2 0
1: 3 4 1 0
1: 4 5 2 0
1: 5 6 1 0
1: 6 7 2 0
1: 7 8 1 0
1: 8 9 2 0
1: 9 10 1 0
1: M END
1:
1: admntn
1: RDKit 2D
1:
1: 10 12 0 0 0 0 0 0 0 0999 V2000
1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 1 0
1: 3 4 1 0
1: 4 5 1 0
1: 5 6 1 0
1: 6 7 1 0
1: 7 8 1 0
1: 8 9 1 0
1: 6 10 1 0
1: 8 1 1 0
1: 9 4 1 0
1: 10 2 1 0
1: M END
1:
1: github 4845 - nan coordinates but no crash
1: RDKit 2D
1:
1: 42 44 0 0 0 0 0 0 0 0999 V2000
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0
1: 1 2 1 0
1: 2 3 1 0
1: 2 4 2 0
1: 4 5 1 0
1: 5 6 3 0
1: 6 7 1 0
1: 7 8 2 0
1: 8 9 1 0
1: 9 10 3 0
1: 10 11 1 0
1: 11 12 2 0
1: 12 13 1 0
1: 13 14 3 0
1: 14 15 1 0
1: 15 16 2 0
1: 16 17 1 0
1: 16 18 1 0
1: 12 19 1 0
1: 19 20 2 0
1: 20 21 1 0
1: 20 22 1 0
1: 19 23 1 0
1: 23 24 3 0
1: 24 25 1 0
1: 25 26 1 0
1: 26 27 2 0
1: 27 28 2 0
1: 26 29 1 0
1: 29 30 3 0
1: 8 31 1 0
1: 31 32 2 0
1: 32 33 1 0
1: 32 34 1 0
1: 31 35 1 0
1: 35 36 3 0
1: 36 37 1 0
1: 37 38 2 0
1: 37 39 1 0
1: 39 40 2 0
1: 40 41 1 0
1: 40 42 1 0
1: 39 4 1 0
1: 15 7 1 0
1: 30 11 1 0
1: M END
1:
47: Randomness seeded to: 3688327896
47: [06:34:54] WARNING: not removing hydrogen atom without neighbors
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
47: [06:34:54] Explicit valence for atom # 1 N, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 1 N, 6, is greater than permitted
47: [06:34:54] Explicit valence for atom # 1 N, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 1 N, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 2 O, 3, is greater than permitted
47: [06:34:54] Explicit valence for atom # 2 O, 3, is greater than permitted
47: [06:34:54] non-ring atom 2 marked aromatic
47: [06:34:54] non-ring atom 2 marked aromatic
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 1 2 3
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 1 2 3
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 0 1 2
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 0 1 2
47: [06:34:54] Explicit valence for atom # 1 O, 3, is greater than permitted
47: [06:34:54] Explicit valence for atom # 4 F, 2, is greater than permitted
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 6 7 8
47: [06:34:54] Explicit valence for atom # 1 C, 5, is greater than permitted
47: [06:34:54] WARNING: not removing hydrogen atom with dummy atom neighbors
47: [06:34:54] WARNING: not removing hydrogen atom with dummy atom neighbors
47: [06:34:54] WARNING: not removing hydrogen atom with wedged bond
47: [06:34:54] WARNING: not removing hydrogen atom without neighbors
47: [06:34:54] WARNING: not removing hydrogen atom without neighbors
47: [06:34:54] WARNING: not removing hydrogen atom without neighbors
47: [06:34:54] WARNING: not removing hydrogen atom without neighbors
47: [06:34:54] Unreasonable formal charge on atom # 0.
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: no atom
47: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: at
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579537249A8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: no owner
47: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
47: Failed Expression: dp_mol
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x0000557953724A32 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: atom not associated with this molecule
47: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: &at->getOwningMol() == this
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x0000557953724AC5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: no atom
47: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: at
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x0000557953724BB0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: no owner
47: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
47: Failed Expression: dp_mol
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x0000557953724C41 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: atom not associated with this molecule
47: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: &at->getOwningMol() == this
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x0000557953724CDD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: no atom
47: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: at
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579537255F9 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: no owner
47: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
47: Failed Expression: dp_mol
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x0000557953724E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: atom not associated with this molecule
47: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: &at->getOwningMol() == this
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x0000557953724EE2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: null atom passed in
47: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: atom_pin
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579537255D1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: cannot take ownership of an atom which already has an owner
47: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579537251F8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: cannot take ownership of an bond which already has an owner
47: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp
47: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579537255AD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
47: [06:34:54] WARNING: not removing hydrogen atom without neighbors
47: [06:34:54] Explicit valence for atom # 1 F greater than permitted
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: plain atoms have no Query
47: Violation occurred on line 691 in file ./Code/GraphMol/Atom.cpp
47: Failed Expression: 0
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::Atom::setQuery(Queries::Query<int, RDKit::Atom const*, true>*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579536CE10B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: plain atoms have no Query
47: Violation occurred on line 696 in file ./Code/GraphMol/Atom.cpp
47: Failed Expression: 0
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::Atom::expandQuery(Queries::Query<int, RDKit::Atom const*, true>*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579536CE1A0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: plain bonds have no Query
47: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp
47: Failed Expression: 0
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::Bond::setQuery(Queries::Query<int, RDKit::Bond const*, true>*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579536CDE30 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54]
47:
47: ****
47: Pre-condition Violation
47: plain bonds have no query
47: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp
47: Failed Expression: 0
47: ----------
47: Stacktrace:
47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
47: 2# RDKit::Bond::expandQuery(Queries::Query<int, RDKit::Bond const*, true>*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
47: 3# 0x00005579536CDEC5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 4# 0x0000557953771CB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 5# 0x00005579537727D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 6# 0x0000557953772C50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 7# 0x00005579537442C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 8# 0x000055795374462C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 9# 0x00005579536C080E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: 10# 0x00007FBEB9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6
47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
47: 12# 0x00005579536C0851 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch
47: ----------
47: ****
47:
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
47: [06:34:54] Unusual charge on atom 0 number of radical electrons set to zero
47: [06:34:54] Unusual charge on atom 0 number of radical electrons set to zero
47: [06:34:54] Unusual charge on atom 0 number of radical electrons set to zero
47: [06:34:54] non-ring atom 0 marked aromatic
47: [06:34:54] non-ring atom 0 marked aromatic
47: [06:34:54] Explicit valence for atom # 1 C, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 9 C, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 3 N, 4, is greater than permitted
47: [06:34:54] Explicit valence for atom # 15 C, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 11 C, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 9 C, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 9 C, 5, is greater than permitted
47: [06:34:54] Explicit valence for atom # 9 C, 6, is greater than permitted
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 7
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 3
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 3 7
47: [06:34:54] Can't kekulize mol. Unkekulized atoms: 3 7
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
47: [06:34:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
48: Randomness seeded to: 2492710307
48: ===============================================================================
48: All tests passed (62 assertions in 6 test cases)
48:
49: Randomness seeded to: 1664261559
49: ===============================================================================
49: All tests passed (136 assertions in 8 test cases)
49:
50: Randomness seeded to: 208729798
50: ===============================================================================
50: All tests passed (283 assertions in 11 test cases)
50:
51: Randomness seeded to: 3352507213
51: [06:34:54] unable to set wavy bonds for double bonds: 3
51: [06:34:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
51: [06:34:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
53: Randomness seeded to: 84790609
53: ===============================================================================
53: All tests passed (14 assertions in 4 test cases)
53:
54: Randomness seeded to: 2083168711
54: ===============================================================================
54: All tests passed (10 assertions in 1 test case)
54:
55: Randomness seeded to: 3406833361
55: ===============================================================================
55: All tests passed (6 assertions in 1 test case)
55:
56: Randomness seeded to: 154740896
56: ===============================================================================
56: All tests passed (45 assertions in 4 test cases)
56:
57: Randomness seeded to: 240868139
57: ===============================================================================
57: All tests passed (7 assertions in 2 test cases)
57:
21/235 Test #1: testCoordGen ........................... Passed 0.20 sec
22/235 Test #37: graphmoltestChirality .................. Passed 0.13 sec
23/235 Test #39: graphmoltestPicklerGlobalSetting ....... Passed 0.13 sec
24/235 Test #40: graphmolIterTest ....................... Passed 0.13 sec
25/235 Test #42: graphmolMemTest1 ....................... Passed 0.12 sec
26/235 Test #44: molBundleTest .......................... Passed 0.11 sec
27/235 Test #45: testSGroup ............................. Passed 0.11 sec
28/235 Test #46: test-valgrind .......................... Passed 0.11 sec
29/235 Test #48: graphmolOrganometallicsCatch ........... Passed 0.10 sec
30/235 Test #49: graphmolSGroupCatch .................... Passed 0.10 sec
31/235 Test #50: graphmolAdjustQueryCatch ............... Passed 0.09 sec
32/235 Test #53: moliteratorTestsCatch .................. Passed 0.09 sec
33/235 Test #54: queryTestsCatch ........................ Passed 0.08 sec
34/235 Test #55: molbundleTestsCatch .................... Passed 0.08 sec
35/235 Test #56: pickleTestsCatch ....................... Passed 0.08 sec
36/235 Test #57: tableTestsCatch ........................ Passed 0.07 sec
test 63
Start 63: smiTestCatch
63: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse
63: Test timeout computed to be: 1500
test 64
Start 64: nontetrahedralCatch
64: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch
64: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse
64: Test timeout computed to be: 1500
test 65
Start 65: v2smiTestCatch
65: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch
65: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse
65: Test timeout computed to be: 1500
test 66
Start 66: testDepictor
66: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor
66: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor
66: Test timeout computed to be: 1500
test 67
Start 67: depictorCatch
67: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch
67: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor
67: Test timeout computed to be: 1500
test 68
Start 68: pyDepictor
68: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap/testDepictor.py"
68: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap
68: Test timeout computed to be: 1500
test 69
Start 69: testMrvToMol
69: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol
69: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse
69: Test timeout computed to be: 1500
test 70
Start 70: fileParsersTest1
70: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
70: Test timeout computed to be: 1500
test 71
Start 71: testAtropisomers
71: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers
71: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
71: Test timeout computed to be: 1500
test 72
Start 72: testSquiggleDoubleBonds
72: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds
72: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
72: Test timeout computed to be: 1500
test 73
Start 73: testMolSupplier
73: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier
73: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
73: Test timeout computed to be: 1500
test 74
Start 74: testGeneralFileReader
74: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader
74: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
74: Test timeout computed to be: 1500
test 75
Start 75: testMultithreadedMolSupplier
75: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier
75: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
75: Test timeout computed to be: 1500
test 76
Start 76: testMolWriter
76: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter
76: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
76: Test timeout computed to be: 1500
test 77
Start 77: testTplParser
77: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser
77: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
77: Test timeout computed to be: 1500
test 78
Start 78: testMol2ToMol
78: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol
78: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
78: Test timeout computed to be: 1500
36: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1
36: [06:34:55] non-ring atom 0 marked aromatic
36: [06:34:55] non-ring atom 0 marked aromatic
36: [06:34:55] Conflicting single bond directions around double bond at index 17.
36: [06:34:55] BondStereo set to STEREONONE and single bond directions set to NONE.
36: starting ring finding
36: done
36: starting ring finding
36: done
36: starting ring finding
14: ......
14: ----------------------------------------------------------------------
14: Ran 6 tests in 0.001s
14:
14: OK
16: .........
16: ----------------------------------------------------------------------
16: Ran 9 tests in 0.003s
16:
16: OK
15: .........
15: ----------------------------------------------------------------------
15: Ran 9 tests in 0.008s
15:
15: OK
38: [06:34:54] done
38: [06:34:54] -------------------------------------
38: [06:34:54] Testing combining molecules using pickles.
38: Atoms:
38: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3
38: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3
38: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3
38: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3
38: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3
38: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3
38: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3
38: Bonds:
38: 0 0->1 order: 1
38: 1 1->2 order: 1
38: 2 2->0 order: 1
38: 3 3->4 order: 1
38: 4 4->5 order: 1
38: 5 5->6 order: 1
38: 6 6->3 order: 1
38: [06:34:54] done
38: [06:34:54] -------------------------------------
38: [06:34:54] Testing Issue164: Roundtrip Pickle Failure.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing Issue219: Pickle Failure with Conformations.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing Issue220: Pickle problems with bond stereochemistry.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing query serialization.
38: [06:34:55] C=[$(C=O)]
38: [06:34:55] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl]
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing radical handling in pickles.
38: [06:34:55] done
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing sf.net issue 2788233.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing sf.net issue 3202580.
38: mass! 13.0034
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing sf.net issue 3316407.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing sf.net issue 3496759.
38: smi match: *C *C
38: smi match: **=* **=*
38: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O
38: smi match: *OS(=O)OC *OS(=O)OC
38: smi match: *S(=O)(=O)OC *S(=O)(=O)OC
38: smi match: O=COC=O O=COC=O
38: smi match: OO OO
38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F
38: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1
38: smi match: nnnOC=O nnnOC=O
38: smi match: *=C=N *=C=N
38: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F
38: smi match: SP(S)=S SP(S)=S
38: smi match: NP(N)(N)=O NP(N)(N)=O
38: smi match: cN=[N+]=[N-] cN=[N+]=[N-]
38: smi match: *CC=O *CC=O
38: smi match: NNC=O NNC=O
38: smi match: * *
38: smi match: C=P C=P
38: smi match: CC(=N)Cl CC(=N)Cl
38: smi match: N=O N=O
38: smi match: ** **
38: smi match: N=C=N N=C=N
38: smi match: [C-]#[NH+] [C-]#[NH+]
38: smi match: O=CON(C=O)C=O O=CON(C=O)C=O
38: smi match: N#CC[OH] N#CC[OH]
38: smi match: N#CC=O N#CC=O
38: smi match: N#CS(=O)=O N#CS(=O)=O
38: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC
38: smi match: N#CN=N N#CN=N
38: smi match: N=NCC=O N=NCC=O
38: smi match: CCCCCCC CCCCCCC
38: smi match: OCCOCCO OCCOCCO
38: smi match: SS SS
38: smi match: [SH] [SH]
38: smi match: *1CC1 *1CC1
38: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH]
38: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH]
38: smi match: NC(=S)N=N NC(=S)N=N
38: smi match: N#CS N#CS
38: smi match: cC[N+] cC[N+]
38: smi match: C*C=S C*C=S
38: smi match: N[CH2]C#N N[CH2]C#N
38: smi match: O=C1CCO1 O=C1CCO1
38: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH]
38: smi match: O=C1CCN1 O=C1CCN1
38: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1
38: smi match: C=CC=CC=CC=C C=CC=CC=CC=C
38: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1
38: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21
38: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1
38: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1
38: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1
38: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2
38: smi match: cN(=O)~O cN(=O)~O
38: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O
38: smi match: N~NC=O N~NC=O
38: smi match: *=N~C *=N~C
38: smi match: CO*(=O)=O CO*(=O)=O
38: smi match: * *
38: smi match: * *
38: smi match: *C=C *C=C
38: smi match: N#CS N#CS
38: smi match: *C=S *C=S
38: smi match: *N *N
38: smi match: *C(=C)C=O *C(=C)C=O
38: smi match: *C#C *C#C
38: smi match: N#CCO N#CCO
38: smi match: O=N(=O)CCO O=N(=O)CCO
38: smi match: N=CS N=CS
38: smi match: O=CNC(O)C=O O=CNC(O)C=O
38: smi match: C=C(C=O)C=O C=C(C=O)C=O
38: smi match: N=CC=O N=CC=O
38: smi match: *C(C=O)C=O *C(C=O)C=O
38: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O
38: smi match: O=CC=CC=O O=CC=CC=O
38: smi match: O=CN(O)C=O O=CN(O)C=O
38: smi match: O=CN(S)C=O O=CN(S)C=O
38: smi match: O=CNC=O O=CNC=O
38: smi match: O=CNN=O O=CNN=O
38: smi match: O=CNNC=O O=CNNC=O
38: smi match: O=CNOC=O O=CNOC=O
38: smi match: O=CS O=CS
38: smi match: O=CSC=S O=CSC=S
38: smi match: S=CS S=CS
38: smi match: C=O C=O
38: smi match: *C=N *C=N
38: smi match: CCCCCCC CCCCCCC
38: smi match: CN=O CN=O
38: smi match: CS(=O)(=O)O CS(=O)(=O)O
38: smi match: O=C1CCO1 O=C1CCO1
38: smi match: C=C(S)[SH]=O C=C(S)[SH]=O
38: smi match: C=CCO C=CCO
38: smi match: C=CC=N C=CC=N
38: smi match: C=CC=O C=CC=O
38: smi match: C=CC(=O)C=C C=CC(=O)C=C
38: smi match: C=CC=S C=CC=S
38: smi match: C=CC(=S)S C=CC(=S)S
38: smi match: *C=C(*)C=C *C=C(*)C=C
38: smi match: C=CC=N C=CC=N
38: smi match: *N(*)C=C *N(*)C=C
38: smi match: C=CN(=O)=O C=CN(=O)=O
38: smi match: C=CN(O)=O C=CN(O)=O
38: smi match: C=CO C=CO
38: smi match: C=COC=O C=COC=O
38: smi match: C=CS C=CS
38: smi match: C=C[SH](=O)=O C=C[SH](=O)=O
38: smi match: C=NCO C=NCO
38: smi match: C=NC=O C=NC=O
38: smi match: C=NN C=NN
38: smi match: C=NN=C C=NN=C
38: smi match: C=NO C=NO
38: smi match: C=NOC=O C=NOC=O
38: smi match: C=N=O C=N=O
38: smi match: N#CS N#CS
38: smi match: *CN=O *CN=O
38: smi match: NCN NCN
38: smi match: ON=CCN=O ON=CCN=O
38: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O
38: smi match: N=C(N)S N=C(N)S
38: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1
38: smi match: NC=S NC=S
38: smi match: NC(N)=S NC(N)=S
38: smi match: C=CN C=CN
38: smi match: NOC=O NOC=O
38: smi match: C1CN1 C1CN1
38: smi match: O=C1NNNN1 O=C1NNNN1
38: smi match: N=C(N)C(=N)N N=C(N)C(=N)N
38: smi match: N=C(N)O N=C(N)O
38: smi match: N=C(N)C(=N)S N=C(N)C(=N)S
38: smi match: *C=N *C=N
38: smi match: N=CC=O N=CC=O
38: smi match: N=CS N=CS
58: Randomness seeded to: 1930167149
58: ===============================================================================
58: All tests passed (79 assertions in 6 test cases)
58:
37/235 Test #58: molopsTestsCatch ....................... Passed 0.08 sec
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] WARNING: not removing hydrogen atom without neighbors
59: [06:34:54] Invalid chiral specification on atom 0
59: [06:34:54] Invalid chiral specification on atom 0
59: [06:34:54] Invalid chiral specification on atom 0
59: [06:34:54] Invalid chiral specification on atom 0
59: [06:34:54] Invalid chiral specification on atom 0
59: [06:34:55] SMILES Parse Error: unclosed ring for input: 'C1.C11.C'
59: [06:34:55] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC'
60: [06:34:54] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO'
60: [06:34:54] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O'
60: [06:34:54] SMILES Parse Error: syntax error while parsing: -
60: [06:34:54] SMILES Parse Error: check for mistakes around position 1:
60: [06:34:54] -
60: [06:34:54] ^
60: [06:34:54] SMILES Parse Error: Failed parsing SMILES '-' for input: '-'
60: [06:34:54] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]'
60: [06:34:54] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C'
60: [06:34:54] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O'
60: [06:34:54] SMILES Parse Error: Failed parsing SMILES '*' for input: '*'
60: [06:34:54] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO'
60: [06:34:54] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O'
60: [06:34:54] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-'
60: [06:34:54] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]'
60: [06:34:54] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C'
60: [06:34:54] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O'
60: [06:34:54] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*'
38/235 Test #60: smiTest2 ............................... Passed 0.07 sec
test 79
Start 79: testSequence
79: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence
79: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
79: Test timeout computed to be: 1500
test 80
Start 80: testExtendedStereoParsing
80: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing
80: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
80: Test timeout computed to be: 1500
36: done
36: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C
36: starting sanitization
38: smi match: N=C=N N=C=N
38: smi match: N=C=O N=C=O
38: smi match: N=C=S N=C=S
38: smi match: NOC(=O)O NOC(=O)O
38: smi match: *C(O)=S *C(O)=S
38: smi match: C=CO C=CO
38: smi match: ON=CC=NO ON=CC=NO
38: smi match: *C[SH](=O)=O *C[SH](=O)=O
38: smi match: OS(=O)=O OS(=O)=O
38: smi match: N#CS N#CS
38: smi match: C=C(S)S C=C(S)S
38: smi match: N=C(N)S N=C(N)S
38: smi match: N=C(S)S N=C(S)S
38: smi match: NC(=S)S NC(=S)S
38: smi match: O=CNS O=CNS
38: smi match: S S
38: smi match: [SiH4] [SiH4]
38: smi match: NS NS
38: smi match: NCN NCN
38: smi match: cC(c)(O)O cC(c)(O)O
38: smi match: *C(c)O *C(c)O
38: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O
38: smi match: cS(=O)(=O)O cS(=O)(=O)O
38: smi match: *c1ccccn1=O *c1ccccn1=O
38: smi match: *c1ccccn1 *c1ccccn1
38: smi match: *c1nccccn1 *c1nccccn1
38: smi match: C1COCOC1 C1COCOC1
38: smi match: C=S C=S
38: smi match: c=S c=S
38: smi match: S=CS S=CS
38: smi match: C=CN(=O)=O C=CN(=O)=O
38: smi match: C=CN(=O)O C=CN(=O)O
13: ......
13: ----------------------------------------------------------------------
13: Ran 6 tests in 0.003s
13:
13: OK
51: [06:34:55] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored.
51: [06:34:55] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored.
51: [06:34:55] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored
51: ===============================================================================
51: All tests passed (2267 assertions in 79 test cases)
51:
29:
29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf...
25: .....
25: ----------------------------------------------------------------------
25: Ran 5 tests in 0.002s
25:
25: OK
25: Testing Alignment Wrapper code:
47: [06:34:55] Explicit valence for atom # 1 O, 3, is greater than permitted
47: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
47: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
47: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
47: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
47: [06:34:55] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point.
47: [06:34:55] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom
47: [06:34:55] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom
47: [06:34:55] non-ring atom 0 marked aromatic
47: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
47: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
28: done
63: Randomness seeded to: 2041067472
63: [06:34:55] SMILES Parse Error: unclosed ring for input: 'c1ccccc'
63: [06:34:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
63: [06:34:55] SMARTS Parse Error: unclosed ring for input: 'c1ccccc'
63: [06:34:55] SMARTS Parse Error: unclosed ring for input: 'C1C'
63: [06:34:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
63: [06:34:55] SMARTS Parse Error: syntax error while parsing: C)foo
63: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo'
63: [06:34:55] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$|
63: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|'
63: [06:34:55] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu'
64: Randomness seeded to: 3249131374
64: [06:34:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
64: [06:34:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
64: [06:34:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
64: [06:34:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
64: [06:34:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
64: [06:34:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
65: Randomness seeded to: 2022052281
65: ===============================================================================
65: All tests passed (14 assertions in 2 test cases)
65:
71: [06:34:55] ---- Running with POSIX locale -----
39/235 Test #13: pyDiscreteValueVect .................... Passed 0.23 sec
40/235 Test #14: pyRealValueVect ........................ Passed 0.23 sec
41/235 Test #15: pySparseIntVect ........................ Passed 0.23 sec
42/235 Test #16: pyFPB .................................. Passed 0.22 sec
43/235 Test #51: chiralityTestsCatch .................... Passed 0.14 sec
44/235 Test #65: v2smiTestCatch ......................... Passed 0.04 sec
test 81
Start 81: fileParsersCatchTest
81: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
81: Test timeout computed to be: 1500
test 82
Start 82: testPropertyLists
82: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists
82: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
82: Test timeout computed to be: 1500
test 83
Start 83: XYZFileParserCatchTest
83: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest
83: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
83: Test timeout computed to be: 1500
test 84
Start 84: cdxmlParserCatchTest
84: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest
84: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
84: Test timeout computed to be: 1500
test 85
Start 85: molfileStereoCatchTest
85: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest
85: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
85: Test timeout computed to be: 1500
test 86
Start 86: connectTheDotsTest
86: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest
86: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
86: Test timeout computed to be: 1500
38: smi match: N=CC=O N=CC=O
38: smi match: C=CS C=CS
38: smi match: SC(S)(S)S SC(S)(S)S
38: smi match: OS(O)(O)O OS(O)(O)O
38: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O
38: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O
38: smi match: N#CS N#CS
38: smi match: C=NO C=NO
38: smi match: C=N[SH]=N C=N[SH]=N
38: smi match: O=C(S)S O=C(S)S
38: smi match: N=C(S)S N=C(S)S
38: smi match: N=C(=N)S N=C(=N)S
38: smi match: O=N=O O=N=O
38: smi match: O=NO O=NO
38: smi match: ONO ONO
38: smi match: C1SCS1 C1SCS1
38: smi match: N=C=S N=C=S
38: smi match: N=C=N N=C=N
38: smi match: C1N=N1 C1N=N1
38: smi match: *CS *CS
38: smi match: SC(S)=C(S)S SC(S)=C(S)S
38: smi match: N=CC=NO N=CC=NO
38: smi match: N#CCC#N N#CCC#N
38: smi match: CON=O CON=O
38: smi match: C=CN C=CN
38: smi match: C=N[SH](=O)=O C=N[SH](=O)=O
38: smi match: NN=O NN=O
38: smi match: NC(=O)S NC(=O)S
38: smi match: N#CS N#CS
38: smi match: NC(=O)C(N)=O NC(=O)C(N)=O
38: smi match: c=N c=N
38: smi match: C1COCO1 C1COCO1
38: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O
38: smi match: O=CC=O O=CC=O
38: smi match: O=CNOC=O O=CNOC=O
38: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1
38: smi match: ONO ONO
38: smi match: ON(~O)~O ON(~O)~O
38: smi match: OC1COC(O)C1 OC1COC(O)C1
38: smi match: OC1CCOC1O OC1CCOC1O
38: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1
38: smi match: N=[N+]=N N=[N+]=N
38: smi match: N#CN N#CN
38: smi match: C=NN=C C=NN=C
38: smi match: *CCN(C)C *CCN(C)C
38: smi match: CNN CNN
38: smi match: *CC *CC
38: smi match: OCS OCS
38: smi match: C1NO1 C1NO1
38: smi match: COS(C)(=O)=O COS(C)(=O)=O
38: smi match: C1CO1 C1CO1
38: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1
38: smi match: *C(*)=C *C(*)=C
38: smi match: N#[NH+] N#[NH+]
38: smi match: C#NO C#NO
38: smi match: OOO OOO
38: smi match: OO OO
38: smi match: O~Cl(~O)~O O~Cl(~O)~O
38: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O
38: smi match: [OH]~C(~O)~O [OH]~C(~O)~O
38: smi match: *N *N
38: smi match: *P *P
38: smi match: *S *S
38: smi match: *C(*)(*)C=C *C(*)(*)C=C
38: smi match: *C(*)(*)C=C *C(*)(*)C=C
38: smi match: *C(*)C=C *C(*)C=C
38: smi match: *CC=C *CC=C
38: smi match: CN=C=O CN=C=O
38: smi match: CN=C=S CN=C=S
38: smi match: *C=O *C=O
38: smi match: N=N N=N
38: smi match: SS SS
38: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1
38: smi match: CSC(C)=N CSC(C)=N
38: smi match: COC(C)=N COC(C)=N
38: smi match: C=C=C C=C=C
38: smi match: *C(=O)OC=O *C(=O)OC=O
38: smi match: C=CC#N C=CC#N
38: smi match: C=CC=O C=CC=O
38: smi match: CC=CC(C)=O CC=CC(C)=O
38: smi match: CC=CC(=O)OCC CC=CC(=O)OCC
38: smi match: C#CC#N C#CC#N
38: smi match: C#CC=O C#CC=O
38: smi match: C#CC(=O)OCC C#CC(=O)OCC
38: smi match: C#CC=O C#CC=O
38: smi match: *C(=O)C#C *C(=O)C#C
38: smi match: C=CC=O C=CC=O
38: smi match: *C(*)(*)O *C(*)(*)O
38: smi match: COS(O)(=O)=O COS(O)(=O)=O
38: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-]
38: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-]
45/235 Test #28: testUFFForceField ...................... Passed 0.22 sec
73: [06:34:55]
73: -----------------------------------------
74: [06:34:55]
74: -----------------------------------------
74: [06:34:55] Finished: testDetermineFormat()
74: [06:34:55] -----------------------------------------
74:
74: [06:34:55]
74: -----------------------------------------
test 87
Start 87: v2MolSuppliers
87: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers
87: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
87: Test timeout computed to be: 1500
38: smi match: *C(*)(*)C=O *C(*)(*)C=O
38: smi match: *C(*)(*)C=O *C(*)(*)C=O
38: smi match: *C(*)C=O *C(*)C=O
38: smi match: *CC=O *CC=O
38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O
38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O
38: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O
38: smi match: *C[SH](=O)=O *C[SH](=O)=O
75: [06:34:55]
75: -----------------------------------------
72: Randomness seeded to: 2294096692
72: ===============================================================================
72: All tests passed (15 assertions in 3 test cases)
72:
2: ....
2: ----------------------------------------------------------------------
2: Ran 4 tests in 0.029s
2:
2: OK
64: [06:34:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
64: [06:34:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry
64: [06:34:55] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false.
64: ===============================================================================
64: All tests passed (308 assertions in 9 test cases)
64:
47: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
47: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
36: done
36: starting sanitization
36: done
36: starting ring finding
36: done
36: starting ring finding
36: done
36: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1
70: ***************************************
70: ***************************************
70: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
70: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
32: ......
32: ----------------------------------------------------------------------
32: Ran 6 tests in 0.001s
32:
32: OK
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
46/235 Test #25: pyAlignment ............................ Passed 0.23 sec
47/235 Test #64: nontetrahedralCatch .................... Passed 0.07 sec
48/235 Test #72: testSquiggleDoubleBonds ................ Passed 0.05 sec
49/235 Test #77: testTplParser .......................... Passed 0.04 sec
test 88
Start 88: v2FileParsersCatchTest
88: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest
88: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
88: Test timeout computed to be: 1500
test 89
Start 89: multithreadedSupplierCatchTest
89: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest
89: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
89: Test timeout computed to be: 1500
test 90
Start 90: testSubstructMatch
90: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch
90: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct
90: Test timeout computed to be: 1500
test 91
Start 91: substructTestCatch
91: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch
91: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct
91: Test timeout computed to be: 1500
38: smi match: * *
38: smi match: *1CC1 *1CC1
38: smi match: O=COC=O O=COC=O
38: smi match: N=C=O N=C=O
38: smi match: N=C=S N=C=S
38: smi match: O~O O~O
38: smi match: N~[SiH4] N~[SiH4]
38: smi match: *P *P
38: smi match: C=N=N C=N=N
38: smi match: *N#[NH+] *N#[NH+]
38: smi match: *S* *S*
38: smi match: ** **
38: smi match: *CC* *CC*
38: smi match: *O[SiH3] *O[SiH3]
38: smi match: *OS(*)~O *OS(*)~O
38: smi match: N~N~O N~N~O
38: smi match: *N(~O)(~O)~O *N(~O)(~O)~O
38: smi match: *[N+](=C)[O-] *[N+](=C)[O-]
38: smi match: * *
38: smi match: *C(*)NCN(*)* *C(*)NCN(*)*
38: smi match: *OCC#N *OCC#N
38: smi match: **C=C **C=C
38: smi match: C=C[O-] C=C[O-]
38: smi match: C=CO C=CO
38: smi match: * *
38: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O
38: smi match: O=COn1ccnc1 O=COn1ccnc1
38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F
38: smi match: CC(C)(C)S CC(C)(C)S
38: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C
38: smi match: [CH]=O [CH]=O
38: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C
38: smi match: SS SS
38: smi match: [SH] [SH]
38: smi match: *C* *C*
38: smi match: * *
38: smi match: C[nH3+] C[nH3+]
38: smi match: cC(=N)[NH2] cC(=N)[NH2]
38: smi match: O=CN[OH] O=CN[OH]
38: smi match: NN NN
38: smi match: * *
38: smi match: *OP(=O)O* *OP(=O)O*
38: smi match: * *
38: smi match: * *
38: smi match: * *
38: smi match: *N=C(*)* *N=C(*)*
38: smi match: *C(*)(*)C=O *C(*)(*)C=O
38: smi match: CSC=O CSC=O
38: smi match: * *
38: smi match: O=CCl O=CCl
38: smi match: *** ***
38: smi match: *C=O *C=O
38: smi match: C[OH] C[OH]
38: smi match: C[OH] C[OH]
38: smi match: C[OH] C[OH]
38: smi match: C[OH] C[OH]
38: smi match: C[CH]=O C[CH]=O
38: smi match: *=* *=*
74: [06:34:55] Finished: testSdf()
74: [06:34:55] -----------------------------------------
74:
74: [06:34:55]
74: -----------------------------------------
74: [06:34:55] Finished: testSmi()
74: [06:34:55] -----------------------------------------
74:
74: [06:34:55]
74: -----------------------------------------
38: smi match: *C *C
70: [06:34:55] bond with order 0 found on line 7. This is not part of the MDL specification.
47: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
47: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
47: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
69: Using new chirality perception
69: Test
69:
69: rxnStereoMarkedCrossed.mrv
69:
69: Test
69:
69: 145323811.mol
69:
69: [06:34:55] unsupported number of radical electrons 5
73: [06:34:55]
73:
73: ****
73: Invariant Violation
73: bad prop value
73: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp
73: Failed Expression: nSwaps < 2
73: ----------
73: Stacktrace:
73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
73: 2# 0x00007FFA5C3947E5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
73: 4# 0x00005586306CA134 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier
73: 5# 0x000055863069FA90 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier
73: 6# 0x00005586306A2DBB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier
73: 7# 0x00007FFA5B833CA8 in /lib/x86_64-linux-gnu/libc.so.6
73: 8# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
73: 9# 0x00005586306A4981 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier
73: ----------
73: ****
73:
79: Sequence: GREG
79: HELM: PEPTIDE1{G.R.E.G}$$$$
79: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O
79: PDB:
79: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O
79: CONECT 1 2
79: CONECT 2 3
79: CONECT 3 4 4 5
79: CONECT 5 6
79: CONECT 6 7 9
79: CONECT 7 8 8 16
79: CONECT 9 10
79: CONECT 10 11
79: CONECT 11 12
79: CONECT 12 13
79: CONECT 13 14 14 15
79: CONECT 16 17
79: CONECT 17 18 20
79: CONECT 18 19 19 25
79: CONECT 20 21
79: CONECT 21 22
79: CONECT 22 23 23 24
79: CONECT 25 26
79: CONECT 26 27
79: CONECT 27 28 28 29
79: END
79:
79: Sequence: TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
79: 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}$$$$
79: 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
79: PDB:
79: ATOM 1 N THR A 1 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 2 CA THR A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 3 C THR A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 4 O THR A 1 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 5 CB THR A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 6 OG1 THR A 1 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 7 CG2 THR A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 8 N THR A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 9 CA THR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 10 C THR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 11 O THR A 2 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 12 CB THR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 13 OG1 THR A 2 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 14 CG2 THR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 15 N CYS A 3 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 16 CA CYS A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 17 C CYS A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 18 O CYS A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 19 CB CYS A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 20 SG CYS A 3 0.000 0.000 0.000 1.00 0.00 S
79: ATOM 21 N CYS A 4 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 22 CA CYS A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 23 C CYS A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 24 O CYS A 4 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 25 CB CYS A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 26 SG CYS A 4 0.000 0.000 0.000 1.00 0.00 S
79: ATOM 27 N PRO A 5 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 28 CA PRO A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 29 C PRO A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 30 O PRO A 5 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 31 CB PRO A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 32 CG PRO A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 33 CD PRO A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 34 N SER A 6 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 35 CA SER A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 36 C SER A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 37 O SER A 6 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 38 CB SER A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 39 OG SER A 6 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 40 N ILE A 7 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 41 CA ILE A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 42 C ILE A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 43 O ILE A 7 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 44 CB ILE A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 45 CG1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 46 CG2 ILE A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 47 CD1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 48 N VAL A 8 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 49 CA VAL A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 50 C VAL A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 51 O VAL A 8 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 52 CB VAL A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 53 CG1 VAL A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 54 CG2 VAL A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 55 N ALA A 9 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 56 CA ALA A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 57 C ALA A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 58 O ALA A 9 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 59 CB ALA A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 60 N ARG A 10 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 61 CA ARG A 10 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 62 C ARG A 10 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 63 O ARG A 10 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 64 CB ARG A 10 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 65 CG ARG A 10 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 66 CD ARG A 10 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 67 NE ARG A 10 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 68 CZ ARG A 10 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 69 NH1 ARG A 10 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 70 NH2 ARG A 10 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 71 N SER A 11 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 72 CA SER A 11 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 73 C SER A 11 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 74 O SER A 11 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 75 CB SER A 11 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 76 OG SER A 11 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 77 N ASN A 12 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 78 CA ASN A 12 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 79 C ASN A 12 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 80 O ASN A 12 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 81 CB ASN A 12 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 82 CG ASN A 12 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 83 OD1 ASN A 12 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 84 ND2 ASN A 12 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 85 N PHE A 13 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 86 CA PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 87 C PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 88 O PHE A 13 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 89 CB PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 90 CG PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 91 CD1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 92 CD2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 93 CE1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 94 CE2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 95 CZ PHE A 13 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 96 N ASN A 14 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 97 CA ASN A 14 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 98 C ASN A 14 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 99 O ASN A 14 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 100 CB ASN A 14 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 101 CG ASN A 14 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 102 OD1 ASN A 14 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 103 ND2 ASN A 14 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 104 N VAL A 15 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 105 CA VAL A 15 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 106 C VAL A 15 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 107 O VAL A 15 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 108 CB VAL A 15 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 109 CG1 VAL A 15 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 110 CG2 VAL A 15 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 111 N CYS A 16 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 112 CA CYS A 16 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 113 C CYS A 16 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 114 O CYS A 16 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 115 CB CYS A 16 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 116 SG CYS A 16 0.000 0.000 0.000 1.00 0.00 S
79: ATOM 117 N ARG A 17 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 118 CA ARG A 17 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 119 C ARG A 17 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 120 O ARG A 17 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 121 CB ARG A 17 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 122 CG ARG A 17 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 123 CD ARG A 17 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 124 NE ARG A 17 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 125 CZ ARG A 17 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 126 NH1 ARG A 17 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 127 NH2 ARG A 17 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 128 N LEU A 18 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 129 CA LEU A 18 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 130 C LEU A 18 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 131 O LEU A 18 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 132 CB LEU A 18 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 133 CG LEU A 18 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 134 CD1 LEU A 18 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 135 CD2 LEU A 18 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 136 N PRO A 19 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 137 CA PRO A 19 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 138 C PRO A 19 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 139 O PRO A 19 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 140 CB PRO A 19 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 141 CG PRO A 19 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 142 CD PRO A 19 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 143 N GLY A 20 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 144 CA GLY A 20 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 145 C GLY A 20 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 146 O GLY A 20 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 147 N THR A 21 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 148 CA THR A 21 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 149 C THR A 21 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 150 O THR A 21 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 151 CB THR A 21 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 152 OG1 THR A 21 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 153 CG2 THR A 21 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 154 N PRO A 22 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 155 CA PRO A 22 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 156 C PRO A 22 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 157 O PRO A 22 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 158 CB PRO A 22 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 159 CG PRO A 22 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 160 CD PRO A 22 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 161 N GLU A 23 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 162 CA GLU A 23 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 163 C GLU A 23 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 164 O GLU A 23 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 165 CB GLU A 23 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 166 CG GLU A 23 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 167 CD GLU A 23 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 168 OE1 GLU A 23 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 169 OE2 GLU A 23 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 170 N ALA A 24 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 171 CA ALA A 24 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 172 C ALA A 24 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 173 O ALA A 24 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 174 CB ALA A 24 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 175 N ILE A 25 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 176 CA ILE A 25 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 177 C ILE A 25 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 178 O ILE A 25 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 179 CB ILE A 25 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 180 CG1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 181 CG2 ILE A 25 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 182 CD1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 183 N CYS A 26 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 184 CA CYS A 26 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 185 C CYS A 26 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 186 O CYS A 26 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 187 CB CYS A 26 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 188 SG CYS A 26 0.000 0.000 0.000 1.00 0.00 S
79: ATOM 189 N ALA A 27 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 190 CA ALA A 27 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 191 C ALA A 27 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 192 O ALA A 27 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 193 CB ALA A 27 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 194 N THR A 28 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 195 CA THR A 28 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 196 C THR A 28 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 197 O THR A 28 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 198 CB THR A 28 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 199 OG1 THR A 28 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 200 CG2 THR A 28 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 201 N TYR A 29 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 202 CA TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 203 C TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 204 O TYR A 29 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 205 CB TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 206 CG TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 207 CD1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 208 CD2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 209 CE1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 210 CE2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 211 CZ TYR A 29 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 212 OH TYR A 29 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 213 N THR A 30 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 214 CA THR A 30 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 215 C THR A 30 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 216 O THR A 30 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 217 CB THR A 30 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 218 OG1 THR A 30 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 219 CG2 THR A 30 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 220 N GLY A 31 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 221 CA GLY A 31 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 222 C GLY A 31 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 223 O GLY A 31 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 224 N CYS A 32 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 225 CA CYS A 32 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 226 C CYS A 32 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 227 O CYS A 32 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 228 CB CYS A 32 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 229 SG CYS A 32 0.000 0.000 0.000 1.00 0.00 S
79: ATOM 230 N ILE A 33 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 231 CA ILE A 33 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 232 C ILE A 33 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 233 O ILE A 33 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 234 CB ILE A 33 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 235 CG1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 236 CG2 ILE A 33 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 237 CD1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 238 N ILE A 34 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 239 CA ILE A 34 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 240 C ILE A 34 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 241 O ILE A 34 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 242 CB ILE A 34 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 243 CG1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 244 CG2 ILE A 34 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 245 CD1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 246 N ILE A 35 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 247 CA ILE A 35 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 248 C ILE A 35 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 249 O ILE A 35 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 250 CB ILE A 35 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 251 CG1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 252 CG2 ILE A 35 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 253 CD1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 254 N PRO A 36 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 255 CA PRO A 36 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 256 C PRO A 36 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 257 O PRO A 36 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 258 CB PRO A 36 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 259 CG PRO A 36 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 260 CD PRO A 36 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 261 N GLY A 37 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 262 CA GLY A 37 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 263 C GLY A 37 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 264 O GLY A 37 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 265 N ALA A 38 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 266 CA ALA A 38 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 267 C ALA A 38 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 268 O ALA A 38 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 269 CB ALA A 38 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 270 N THR A 39 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 271 CA THR A 39 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 272 C THR A 39 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 273 O THR A 39 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 274 CB THR A 39 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 275 OG1 THR A 39 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 276 CG2 THR A 39 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 277 N CYS A 40 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 278 CA CYS A 40 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 279 C CYS A 40 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 280 O CYS A 40 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 281 CB CYS A 40 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 282 SG CYS A 40 0.000 0.000 0.000 1.00 0.00 S
79: ATOM 283 N PRO A 41 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 284 CA PRO A 41 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 285 C PRO A 41 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 286 O PRO A 41 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 287 CB PRO A 41 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 288 CG PRO A 41 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 289 CD PRO A 41 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 290 N GLY A 42 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 291 CA GLY A 42 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 292 C GLY A 42 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 293 O GLY A 42 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 294 N ASP A 43 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 295 CA ASP A 43 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 296 C ASP A 43 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 297 O ASP A 43 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 298 CB ASP A 43 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 299 CG ASP A 43 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 300 OD1 ASP A 43 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 301 OD2 ASP A 43 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 302 N TYR A 44 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 303 CA TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 304 C TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 305 O TYR A 44 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 306 CB TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 307 CG TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 308 CD1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 309 CD2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 310 CE1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 311 CE2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 312 CZ TYR A 44 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 313 OH TYR A 44 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 314 N ALA A 45 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 315 CA ALA A 45 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 316 C ALA A 45 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 317 O ALA A 45 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 318 CB ALA A 45 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 319 N ASN A 46 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 320 CA ASN A 46 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 321 C ASN A 46 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 322 O ASN A 46 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 323 CB ASN A 46 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 324 CG ASN A 46 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 325 OD1 ASN A 46 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 326 ND2 ASN A 46 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 327 OXT ASN A 46 0.000 0.000 0.000 1.00 0.00 O
79: CONECT 1 2
79: CONECT 2 3 5
79: CONECT 3 4 4 8
79: CONECT 5 6 7
79: CONECT 8 9
79: CONECT 9 10 12
79: CONECT 10 11 11 15
79: CONECT 12 13 14
79: CONECT 15 16
79: CONECT 16 17 19
79: CONECT 17 18 18 21
79: CONECT 19 20
79: CONECT 21 22
79: CONECT 22 23 25
79: CONECT 23 24 24 27
79: CONECT 25 26
79: CONECT 27 28 33
79: CONECT 28 29 31
79: CONECT 29 30 30 34
79: CONECT 31 32
79: CONECT 32 33
79: CONECT 34 35
79: CONECT 35 36 38
79: CONECT 36 37 37 40
79: CONECT 38 39
79: CONECT 40 41
79: CONECT 41 42 44
79: CONECT 42 43 43 48
79: CONECT 44 45 46
79: CONECT 46 47
79: CONECT 48 49
79: CONECT 49 50 52
79: CONECT 50 51 51 55
79: CONECT 52 53 54
79: CONECT 55 56
79: CONECT 56 57 59
79: CONECT 57 58 58 60
79: CONECT 60 61
79: CONECT 61 62 64
79: CONECT 62 63 63 71
79: CONECT 64 65
79: CONECT 65 66
79: CONECT 66 67
79: CONECT 67 68
79: CONECT 68 69 69 70
79: CONECT 71 72
79: CONECT 72 73 75
79: CONECT 73 74 74 77
79: CONECT 75 76
79: CONECT 77 78
79: CONECT 78 79 81
79: CONECT 79 80 80 85
79: CONECT 81 82
79: CONECT 82 83 83 84
79: CONECT 85 86
79: CONECT 86 87 89
79: CONECT 87 88 88 96
79: CONECT 89 90
79: CONECT 90 91 91 92
79: CONECT 91 93
79: CONECT 92 94 94
79: CONECT 93 95 95
79: CONECT 94 95
79: CONECT 96 97
79: CONECT 97 98 100
79: CONECT 98 99 99 104
79: CONECT 100 101
79: CONECT 101 102 102 103
79: CONECT 104 105
79: CONECT 105 106 108
79: CONECT 106 107 107 111
79: CONECT 108 109 110
79: CONECT 111 112
79: CONECT 112 113 115
79: CONECT 113 114 114 117
79: CONECT 115 116
79: CONECT 117 118
79: CONECT 118 119 121
79: CONECT 119 120 120 128
79: CONECT 121 122
79: CONECT 122 123
79: CONECT 123 124
79: CONECT 124 125
79: CONECT 125 126 126 127
79: CONECT 128 129
79: CONECT 129 130 132
79: CONECT 130 131 131 136
79: CONECT 132 133
79: CONECT 133 134 135
79: CONECT 136 137 142
79: CONECT 137 138 140
79: CONECT 138 139 139 143
79: CONECT 140 141
79: CONECT 141 142
79: CONECT 143 144
79: CONECT 144 145
79: CONECT 145 146 146 147
79: CONECT 147 148
79: CONECT 148 149 151
79: CONECT 149 150 150 154
79: CONECT 151 152 153
79: CONECT 154 155 160
79: CONECT 155 156 158
79: CONECT 156 157 157 161
79: CONECT 158 159
79: CONECT 159 160
79: CONECT 161 162
79: CONECT 162 163 165
79: CONECT 163 164 164 170
79: CONECT 165 166
79: CONECT 166 167
79: CONECT 167 168 168 169
79: CONECT 170 171
79: CONECT 171 172 174
79: CONECT 172 173 173 175
79: CONECT 175 176
79: CONECT 176 177 179
79: CONECT 177 178 178 183
79: CONECT 179 180 181
79: CONECT 181 182
79: CONECT 183 184
79: CONECT 184 185 187
79: CONECT 185 186 186 189
79: CONECT 187 188
79: CONECT 189 190
79: CONECT 190 191 193
79: CONECT 191 192 192 194
79: CONECT 194 195
79: CONECT 195 196 198
79: CONECT 196 197 197 201
79: CONECT 198 199 200
79: CONECT 201 202
79: CONECT 202 203 205
79: CONECT 203 204 204 213
79: CONECT 205 206
79: CONECT 206 207 207 208
79: CONECT 207 209
79: CONECT 208 210 210
79: CONECT 209 211 211
79: CONECT 210 211
79: CONECT 211 212
79: CONECT 213 214
79: CONECT 214 215 217
79: CONECT 215 216 216 220
79: CONECT 217 218 219
79: CONECT 220 221
79: CONECT 221 222
79: CONECT 222 223 223 224
79: CONECT 224 225
79: CONECT 225 226 228
79: CONECT 226 227 227 230
79: CONECT 228 229
79: CONECT 230 231
79: CONECT 231 232 234
79: CONECT 232 233 233 238
79: CONECT 234 235 236
79: CONECT 236 237
79: CONECT 238 239
79: CONECT 239 240 242
79: CONECT 240 241 241 246
79: CONECT 242 243 244
79: CONECT 244 245
79: CONECT 246 247
79: CONECT 247 248 250
79: CONECT 248 249 249 254
79: CONECT 250 251 252
79: CONECT 252 253
79: CONECT 254 255 260
79: CONECT 255 256 258
79: CONECT 256 257 257 261
79: CONECT 258 259
79: CONECT 259 260
79: CONECT 261 262
79: CONECT 262 263
79: CONECT 263 264 264 265
79: CONECT 265 266
79: CONECT 266 267 269
79: CONECT 267 268 268 270
79: CONECT 270 271
79: CONECT 271 272 274
79: CONECT 272 273 273 277
79: CONECT 274 275 276
79: CONECT 277 278
79: CONECT 278 279 281
79: CONECT 279 280 280 283
79: CONECT 281 282
79: CONECT 283 284 289
79: CONECT 284 285 287
79: CONECT 285 286 286 290
79: CONECT 287 288
79: CONECT 288 289
79: CONECT 290 291
79: CONECT 291 292
79: CONECT 292 293 293 294
79: CONECT 294 295
79: CONECT 295 296 298
79: CONECT 296 297 297 302
79: CONECT 298 299
79: CONECT 299 300 300 301
79: CONECT 302 303
79: CONECT 303 304 306
79: CONECT 304 305 305 314
79: CONECT 306 307
79: CONECT 307 308 308 309
79: CONECT 308 310
79: CONECT 309 311 311
79: CONECT 310 312 312
79: CONECT 311 312
79: CONECT 312 313
79: CONECT 314 315
79: CONECT 315 316 318
79: CONECT 316 317 317 319
79: CONECT 319 320
79: CONECT 320 321 323
79: CONECT 321 322 322 327
79: CONECT 323 324
79: CONECT 324 325 325 326
79: END
79:
79: Sequence: GREG
79: HELM: PEPTIDE1{G.R.E.G}$$$$
79: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O
79: PDB:
79: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O
79: CONECT 1 2
79: CONECT 2 3
79: CONECT 3 4 4 5
79: CONECT 5 6
79: CONECT 6 7 9
79: CONECT 7 8 8 16
79: CONECT 9 10
79: CONECT 10 11
79: CONECT 11 12
79: CONECT 12 13
79: CONECT 13 14 14 15
79: CONECT 16 17
79: CONECT 17 18 20
79: CONECT 18 19 19 25
79: CONECT 20 21
79: CONECT 21 22
79: CONECT 22 23 23 24
79: CONECT 25 26
79: CONECT 26 27
79: CONECT 27 28 28 29
79: END
79:
79: Sequence: CYIQNCPLG
79: HELM: PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$
79: 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
79: PDB:
79: ATOM 1 N CYS A 1 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 2 CA CYS A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 3 C CYS A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 4 O CYS A 1 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 5 CB CYS A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 6 SG CYS A 1 0.000 0.000 0.000 1.00 0.00 S
79: ATOM 7 N TYR A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 8 CA TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 9 C TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 10 O TYR A 2 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 11 CB TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 12 CG TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 13 CD1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 14 CD2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 15 CE1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 16 CE2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 17 CZ TYR A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 18 OH TYR A 2 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 19 N ILE A 3 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 20 CA ILE A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 21 C ILE A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 22 O ILE A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 23 CB ILE A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 24 CG1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 25 CG2 ILE A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 26 CD1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 27 N GLN A 4 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 28 CA GLN A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 29 C GLN A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 30 O GLN A 4 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 31 CB GLN A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 38 C ASN A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 39 O ASN A 5 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 40 CB ASN A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 41 CG ASN A 5 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 42 OD1 ASN A 5 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 43 ND2 ASN A 5 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 44 N CYS A 6 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 45 CA CYS A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 46 C CYS A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 47 O CYS A 6 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 48 CB CYS A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 49 SG CYS A 6 0.000 0.000 0.000 1.00 0.00 S
79: ATOM 50 N PRO A 7 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 51 CA PRO A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 52 C PRO A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 53 O PRO A 7 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 54 CB PRO A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 55 CG PRO A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 56 CD PRO A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 57 N LEU A 8 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 58 CA LEU A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 59 C LEU A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 60 O LEU A 8 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 61 CB LEU A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 62 CG LEU A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 63 CD1 LEU A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 64 CD2 LEU A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 65 N GLY A 9 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 66 CA GLY A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 67 C GLY A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 68 O GLY A 9 0.000 0.000 0.000 1.00 0.00 O
79: HETATM 69 N NH2 A 10 0.000 0.000 0.000 1.00 0.00 N
79: CONECT 1 2
79: CONECT 2 3 5
79: CONECT 3 4 4 7
79: CONECT 5 6
79: CONECT 6 49
79: CONECT 7 8
79: CONECT 8 9 11
79: CONECT 9 10 10 19
79: CONECT 11 12
79: CONECT 12 13 13 14
79: CONECT 13 15
79: CONECT 14 16 16
79: CONECT 15 17 17
79: CONECT 16 17
79: CONECT 17 18
79: CONECT 19 20
79: CONECT 20 21 23
79: CONECT 21 22 22 27
79: CONECT 23 24 25
79: CONECT 25 26
79: CONECT 27 28
79: CONECT 28 29 31
79: CONECT 29 30 30 36
79: CONECT 31 32
79: CONECT 32 33
79: CONECT 33 34 34 35
79: CONECT 36 37
79: CONECT 37 38 40
79: CONECT 38 39 39 44
79: CONECT 40 41
79: CONECT 41 42 42 43
79: CONECT 44 45
79: CONECT 45 46 48
79: CONECT 46 47 47 50
79: CONECT 48 49
79: CONECT 50 51 56
79: CONECT 51 52 54
79: CONECT 52 53 53 57
79: CONECT 54 55
79: CONECT 55 56
79: CONECT 57 58
79: CONECT 58 59 61
79: CONECT 59 60 60 65
79: CONECT 61 62
79: CONECT 62 63 64
79: CONECT 65 66
79: CONECT 66 67
79: CONECT 67 68 68 69
79: END
79:
79: Sequence: LfPVXLfPVX
79: HELM: PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$
79: 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
79: PDB:
79: ATOM 1 N LEU A 1 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 2 CA LEU A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 3 C LEU A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 4 O LEU A 1 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 5 CB LEU A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 6 CG LEU A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 7 CD1 LEU A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 8 CD2 LEU A 1 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 9 N DPN A 2 0.000 0.000 0.000 1.00 0.00 N
79: HETATM 10 CA DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 11 C DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 12 O DPN A 2 0.000 0.000 0.000 1.00 0.00 O
79: HETATM 13 CB DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 14 CG DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 15 CD1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 16 CD2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 17 CE1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 18 CE2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 19 CZ DPN A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 20 N PRO A 3 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 21 CA PRO A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 22 C PRO A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 23 O PRO A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 24 CB PRO A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 25 CG PRO A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 26 CD PRO A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 27 N VAL A 4 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 28 CA VAL A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 29 C VAL A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 30 O VAL A 4 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 31 CB VAL A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 32 CG1 VAL A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 33 CG2 VAL A 4 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 34 N ORN A 5 0.000 0.000 0.000 1.00 0.00 N
79: HETATM 35 CA ORN A 5 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 36 C ORN A 5 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 37 O ORN A 5 0.000 0.000 0.000 1.00 0.00 O
79: HETATM 38 CB ORN A 5 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 39 CG ORN A 5 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 40 CD ORN A 5 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 41 NE ORN A 5 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 42 N LEU A 6 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 43 CA LEU A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 44 C LEU A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 45 O LEU A 6 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 46 CB LEU A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 47 CG LEU A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N
79: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O
79: HETATM 54 CB DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 55 CG DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 56 CD1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 57 CD2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 58 CE1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 59 CE2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 60 CZ DPN A 7 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 61 N PRO A 8 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 62 CA PRO A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 63 C PRO A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 64 O PRO A 8 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 65 CB PRO A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 66 CG PRO A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 67 CD PRO A 8 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 68 N VAL A 9 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 69 CA VAL A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 70 C VAL A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 71 O VAL A 9 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 72 CB VAL A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 73 CG1 VAL A 9 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 74 CG2 VAL A 9 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 75 N ORN A 10 0.000 0.000 0.000 1.00 0.00 N
79: HETATM 76 CA ORN A 10 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 77 C ORN A 10 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 78 O ORN A 10 0.000 0.000 0.000 1.00 0.00 O
79: HETATM 79 CB ORN A 10 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 80 CG ORN A 10 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 81 CD ORN A 10 0.000 0.000 0.000 1.00 0.00 C
79: HETATM 82 NE ORN A 10 0.000 0.000 0.000 1.00 0.00 N
79: CONECT 1 2 77
79: CONECT 2 3 5
79: CONECT 3 4 4 9
79: CONECT 5 6
79: CONECT 6 7 8
79: CONECT 9 10
79: CONECT 10 11 13
79: CONECT 11 12 12 20
79: CONECT 13 14
79: CONECT 14 15 15 16
79: CONECT 15 17
79: CONECT 16 18 18
79: CONECT 17 19 19
79: CONECT 18 19
79: CONECT 20 21 26
79: CONECT 21 22 24
79: CONECT 22 23 23 27
79: CONECT 24 25
79: CONECT 25 26
79: CONECT 27 28
79: CONECT 28 29 31
79: CONECT 29 30 30 34
79: CONECT 31 32 33
79: CONECT 34 35
79: CONECT 35 36 38
79: CONECT 36 37 37 42
79: CONECT 38 39
79: CONECT 39 40
79: CONECT 40 41
79: CONECT 42 43
79: CONECT 43 44 46
79: CONECT 44 45 45 50
79: CONECT 46 47
79: CONECT 47 48 49
79: CONECT 50 51
79: CONECT 51 52 54
79: CONECT 52 53 53 61
79: CONECT 54 55
79: CONECT 55 56 56 57
79: CONECT 56 58
79: CONECT 57 59 59
79: CONECT 58 60 60
79: CONECT 59 60
79: CONECT 61 62 67
79: CONECT 62 63 65
79: CONECT 63 64 64 68
79: CONECT 65 66
79: CONECT 66 67
79: CONECT 68 69
79: CONECT 69 70 72
79: CONECT 70 71 71 75
79: CONECT 72 73 74
79: CONECT 75 76
79: CONECT 76 77 79
79: CONECT 77 78 78
79: CONECT 79 80
79: CONECT 80 81
79: CONECT 81 82
79: END
79:
79: Sequence: GREG
79: HELM: PEPTIDE1{G.R.E.G}$$$$
79: Smiles: N=C(N)NCCCC(NC(=O)CN)C(=O)NC(CCC(=O)O)C(=O)NCC(=O)O
79: PDB:
79: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 23 OD1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 24 OD2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N
79: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C
79: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O
79: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O
79: CONECT 1 2
79: CONECT 2 3
79: CONECT 3 4 4 5
79: CONECT 5 6
79: CONECT 6 7 9
79: CONECT 7 8 8 16
79: CONECT 9 10
79: CONECT 10 11
79: CONECT 11 12
79: CONECT 12 13
79: CONECT 13 14 14 15
79: CONECT 16 17
79: CONECT 17 18 20
79: CONECT 18 19 19 25
79: CONECT 20 21
79: CONECT 21 22
79: CONECT 22 23 23 24
79: CONECT 25 26
79: CONECT 26 27
79: CONECT 27 28 28 29
79: END
79:
21: ....................
21: ----------------------------------------------------------------------
21: Ran 20 tests in 0.056s
21:
21: OK
21: Testing Geometry wrapper
83: Randomness seeded to: 1818489859
83: ===============================================================================
83: All tests passed (100 assertions in 2 test cases)
83:
82: Randomness seeded to: 3467418895
82: ===============================================================================
82: All tests passed (95 assertions in 4 test cases)
82:
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
36: [06:34:55] WARNING: not removing hydrogen atom with dummy atom neighbors
36: -------------------------------
36: [06:34:55] Explicit valence for atom # 0 N, 4, is greater than permitted
50/235 Test #78: testMol2ToMol .......................... Passed 0.06 sec
51/235 Test #79: testSequence ........................... Passed 0.05 sec
52/235 Test #80: testExtendedStereoParsing .............. Passed 0.05 sec
53/235 Test #82: testPropertyLists ...................... Passed 0.05 sec
54/235 Test #83: XYZFileParserCatchTest ................. Passed 0.04 sec
38: smi match: C#C C#C
38: smi match: *[CH]C=C *[CH]C=C
38: smi match: cCC(=O)[OH] cCC(=O)[OH]
38: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH]
38: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH]
38: smi match: C=CC(=O)[OH] C=CC(=O)[OH]
38: smi match: N#CC(=O)[OH] N#CC(=O)[OH]
38: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O
38: smi match: *N(*)C*=O *N(*)C*=O
38: smi match: O=*C[OH] O=*C[OH]
38: smi match: *=C*=O *=C*=O
38: smi match: *=CC#N *=CC#N
38: smi match: *C[OH] *C[OH]
38: smi match: ** **
38: smi match: *C[OH] *C[OH]
38: smi match: *C(*)=O *C(*)=O
38: smi match: * *
38: smi match: *CC(=O)[OH] *CC(=O)[OH]
38: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O
70: [06:34:55] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7)
70: [06:34:55] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7)
70: [06:34:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
47: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
47: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
47: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
47: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
47: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29
81: Randomness seeded to: 4196774060
81: [06:34:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 29
81: [06:34:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 28
81: [06:34:55] Could not infer missing lvIdx on malformed SAP line for SGroup 1
81: [06:34:55] SGroup 1 is invalid and will be ignored
81: [06:34:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 28
81: [06:34:55] Could not infer missing lvIdx on malformed SAP line for SGroup 1
81: [06:34:55] SGroup 1 is invalid and will be ignored
81: [06:34:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 35
81: [06:34:55] SGroup SAP line too short: 'M SAP 2 1 12' on line 39
81: [06:34:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 34
81: [06:34:55] SGroup SAP line too short: 'M SAP 2 1 12' on line 38
81: [06:34:55] Could not infer missing lvIdx on malformed SAP line for SGroup 1
81: [06:34:55] SGroup 1 is invalid and will be ignored
81: [06:34:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 34
81: [06:34:55] SGroup SAP line too short: 'M SAP 2 1 12' on line 39
81: [06:34:55] Could not infer missing lvIdx on malformed SAP line for SGroup 1
81: [06:34:55] SGroup 1 is invalid and will be ignored
81: [06:34:55] SGroup 3 referenced on line 40 not found.
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: no bonds
81: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp
81: Failed Expression: !d_bonds.empty()
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map<int, RDKit::SubstanceGroup, std::less<int>, std::allocator<std::pair<int const, RDKit::SubstanceGroup> > >&, RDKit::RWMol*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# 0x00007FB4CC0DA81E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# 0x000055A227C02769 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 16# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] SGroup 3 referenced on line 40 not found.
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: no bonds
81: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp
81: Failed Expression: !d_bonds.empty()
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map<int, RDKit::SubstanceGroup, std::less<int>, std::allocator<std::pair<int const, RDKit::SubstanceGroup> > >&, RDKit::RWMol*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# 0x00007FB4CC0DA81E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# 0x000055A227C02812 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 16# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] no bonds
81: [06:34:55] SGroup 1 is invalid and will be ignored
81: [06:34:55] SGroup line too short: 'M SBV 1 6' on line 42
81: [06:34:55] SGroup 1 is invalid and will be ignored
59: --C1CCC2(CC1)CCCCC2CCC1CCCC1
55/235 Test #2: pyCoordGen ............................. Passed 0.30 sec
test 92
Start 92: testGenericGroups
92: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups
92: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups
92: Test timeout computed to be: 1500
test 93
Start 93: testReaction
93: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction
93: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions
93: Test timeout computed to be: 1500
test 94
Start 94: testReactionFingerprints
94: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints
94: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions
94: Test timeout computed to be: 1500
test 95
Start 95: testEnumeration
95: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration
95: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions
95: Test timeout computed to be: 1500
test 96
Start 96: rxnTestCatch
96: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch
96: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions
96: Test timeout computed to be: 1500
56/235 Test #32: pyDistGeom ............................. Passed 0.26 sec
62: [06:34:55] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC
62: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC'
62: [06:34:55] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON
62: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON'
62: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
62: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
86: Randomness seeded to: 1997655322
86: ===============================================================================
86: All tests passed (8 assertions in 1 test case)
86:
38: smi match: *c *c
38: smi match: CN(C)c CN(C)c
38: smi match: c c
38: smi match: *c *c
38: smi match: *c *c
38: smi match: **:*cF **:*cF
38: smi match: cB([OH])[OH] cB([OH])[OH]
38: smi match: N~N~N N~N~N
38: smi match: *N=N* *N=N*
38: smi match: *CC[OH] *CC[OH]
38: smi match: *CC[OH] *CC[OH]
38: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH]
38: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH]
38: smi match: *CCC(=O)[OH] *CCC(=O)[OH]
38: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH]
38: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O
38: smi match: *OC(*)=O *OC(*)=O
38: smi match: *C(=O)[OH] *C(=O)[OH]
38: smi match: O=C[OH] O=C[OH]
38: smi match: *OC(=O)O* *OC(=O)O*
38: smi match: * *
38: smi match: *OC(=O)Cl *OC(=O)Cl
38: smi match: *C#N *C#N
38: smi match: NCC(=O)NCC=O NCC(=O)NCC=O
38: smi match: SS SS
38: smi match: * *
38: smi match: *=* *=*
38: smi match: *=* *=*
38: smi match: *=* *=*
38: smi match: *=* *=*
38: smi match: C1CO1 C1CO1
38: smi match: *OC(*)=O *OC(*)=O
38: smi match: * *
38: smi match: *O*[OH] *O*[OH]
38: smi match: COC(C)(C)O COC(C)(C)O
38: smi match: *[OH] *[OH]
38: smi match: ** **
38: smi match: C=N[NH2] C=N[NH2]
38: smi match: C=NC=O C=NC=O
38: smi match: * *
38: smi match: C#NC C#NC
38: smi match: CN=C=O CN=C=O
38: smi match: CN=C=S CN=C=S
38: smi match: *OC(*)(*)O* *OC(*)(*)O*
70: generating smiles
70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2
70: converting back
70: check isomorphism
47: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21
81: [06:34:55] SGroup line too short: 'M SBL 2 3 9 10' on line 46
81: [06:34:55] SGroup 2 is invalid and will be ignored
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_bondBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map<int, RDKit::SubstanceGroup, std::less<int>, std::allocator<std::pair<int const, RDKit::SubstanceGroup> > >&, RDKit::RWMol*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0DA6AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# 0x000055A227C033D2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 17# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_bondBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map<int, RDKit::SubstanceGroup, std::less<int>, std::allocator<std::pair<int const, RDKit::SubstanceGroup> > >&, RDKit::RWMol*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0DA6AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# 0x000055A227C0347A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 17# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] bookmark not found
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bond is not part of the SubstanceGroup
81: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp
81: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end()
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map<int, RDKit::SubstanceGroup, std::less<int>, std::allocator<std::pair<int const, RDKit::SubstanceGroup> > >&, RDKit::RWMol*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0DA81E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# 0x000055A227C0347A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 17# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] bond is not part of the SubstanceGroup
81: [06:34:55] SGroup 2 is invalid and will be ignored
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_atomBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map<int, RDKit::SubstanceGroup, std::less<int>, std::allocator<std::pair<int const, RDKit::SubstanceGroup> > >&, RDKit::RWMol*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0DA6AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# 0x000055A227C037E9 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 17# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_atomBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map<int, RDKit::SubstanceGroup, std::less<int>, std::allocator<std::pair<int const, RDKit::SubstanceGroup> > >&, RDKit::RWMol*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0DA6AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# 0x000055A227C03891 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 17# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] bookmark not found
81: [06:34:55] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup.
81: [06:34:55] SGroup 2 is invalid and will be ignored
81: [06:34:55] WARNING: final character of V3000 array is not ')'
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_bondBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227C010F3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] WARNING: final character of V3000 array is not ')'
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_bondBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227C0118B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] bookmark not found
81: [06:34:55] SGroup 1 is invalid and will be ignored
81: [06:34:55] WARNING: final character of V3000 array is not ')'
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_atomBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227C014F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] WARNING: final character of V3000 array is not ')'
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_atomBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227C0158C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] bookmark not found
81: [06:34:55] SGroup 1 is invalid and will be ignored
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_bondBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227C018F3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_bondBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227C0198C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] bookmark not found
81: [06:34:55] SGroup 2 is invalid and will be ignored
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_atomBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227C01CF2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: bookmark not found
81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: (lu != d_atomBookmarks.end())
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227C01D8C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] bookmark not found
81: [06:34:55] SGroup 2 is invalid and will be ignored
test 97
Start 97: pyChemReactions
97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py"
97: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap
97: Test timeout computed to be: 1500
test 98
Start 98: pyChemReactionEnumerations
98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py"
98: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap
98: Test timeout computed to be: 1500
57/235 Test #62: smaTest1 ............................... Passed 0.16 sec
58/235 Test #86: connectTheDotsTest ..................... Passed 0.07 sec
90: ----------------- Test 1
90: Done
90:
90: ----------------- Test 2
90: Done
90:
90: ----------------- Test 3
90: Done
90:
90: ----------------- Test 4
90: Done
90:
90: ----------------- Test 5
90: Done
90:
90: ----------------- Test 5 QueryRoot
90: Done
90:
90: ----------------- Test 6 (Issue71 related)
90: Done
90:
90: ----------------- Testing serial numbers on recursive queries
90: Done
90:
90: [06:34:55] -------------------------------------
90: [06:34:55] Test multithreading
90: reading molecules
85: Randomness seeded to: 245034842
85: [06:34:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored.
85: [06:34:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored.
85: [06:34:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored.
85: [06:34:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored.
85: ===============================================================================
85: All tests passed (142 assertions in 6 test cases)
85:
59/235 Test #85: molfileStereoCatchTest ................. Passed 0.07 sec
61: Randomness seeded to: 1402234417
61: Test
61:
61: ShortAtropisomerNoCoords.cxsmi
61:
61: Test
61:
61: ShortAtropisomer.cxsmi
61:
61: Test
61:
61: ShortAtropisomerArom.cxsmi
61:
61: Test
61:
61: AtropManyChirals.cxsmi
61:
61: Test
61:
61: AtropManyChiralsEnhanced.cxsmi
61:
61: Test
61:
61: AtropManyChiralsEnhanced2.cxsmi
61:
61: Test
61:
61: AtropManyChiralsEnhanced3.cxsmi
61:
61: Test
61:
61: AtropManyChiralsEnhanced4.cxsmi
61:
61: Test
61:
61: BMS-986142_3d_chiral.cxsmi
61:
61: Test
61:
61: BMS-986142_3d.cxsmi
61:
61: Test
61:
61: BMS-986142_atrop1.cxsmi
61:
61: Test
61:
61: BMS-986142_atrop2.cxsmi
61:
61: Test
61:
61: BMS-986142_atrop3.cxsmi
61:
61: Test
61:
61: BMS-986142_atrop4.cxsmi
61:
61: Test
61:
61: BMS-986142_atrop5.cxsmi
61:
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: Test
61:
61: BMS-986142_atrop6.cxsmi
61:
61: Test
61:
61: BMS-986142_atropBad1.cxsmi
61:
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7
61: Test
61:
61: BMS-986142_atropBad2.cxsmi
61:
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7
36: [06:34:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
36: [06:34:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10
36: [06:34:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
36: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
36: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
36: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
36: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
36: [06:34:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged
36:
36: [06:34:55] WARNING: not removing hydrogen atom with dummy atom neighbors
84: Randomness seeded to: 2035038269
84: [06:34:55] Invalid or missing fragment id from CDXML fragment, assigning new one...
84: [06:34:55] Explicit valence for atom # 3 N, 4, is greater than permitted
84: [06:34:55] CDXMLParser: failed sanitizing skipping fragment 32
84: [06:34:55] Bad bond in CDXML skipping fragment 58...
84: [06:34:55] Invalid or missing fragment id from CDXML fragment, assigning new one...
84: [06:34:55] Bad bond in CDXML skipping fragment 58...
87: Randomness seeded to: 4036070803
87: ===============================================================================
87: All tests passed (12 assertions in 5 test cases)
87:
60/235 Test #87: v2MolSuppliers ......................... Passed 0.06 sec
69: Test
69:
69: NewChiralTest.sdf
69:
69: Test
69:
69: NewChiralTest.sdf
69:
69: Test
69:
69: NewChiralTestNoChiral.sdf
69:
69: Test
69:
69: NewChiralTestNoChiral.sdf
69:
69: Test
69:
69: NewChiralTestAllChiral.sdf
69:
69: Test
69:
69: NewChiralTestAllChiral.sdf
69:
69: Test
69:
69: vendor839.sdf
69:
69: Test
69:
69: ProblemShort.mol
69:
69: [06:34:55] For a MultipleSgroup expansion, the matching orphaned bond was not found
69: The multiple sgroup will be ignored
88: Randomness seeded to: 2684408635
88: ===============================================================================
88: All tests passed (6 assertions in 1 test case)
88:
38: smi match: *C(*)=O *C(*)=O
38: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C
38: smi match: *~*=O *~*=O
38: smi match: *~*=O *~*=O
38: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH]
38: smi match: * *
38: smi match: *C#N *C#N
38: smi match: *N(=O)~O *N(=O)~O
38: smi match: N N
38: smi match: OC(=O)C(O)=O OC(=O)C(O)=O
38: smi match: C=NO C=NO
38: smi match: O~O O~O
38: smi match: c[OH] c[OH]
38: smi match: O=P(~[OH])~O O=P(~[OH])~O
38: smi match: CO~P(=O)~O CO~P(=O)~O
38: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O
38: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O
38: smi match: O=P(~O)~O O=P(~O)~O
38: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O
38: smi match: C[NH2] C[NH2]
38: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1
38: smi match: * *
38: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1
38: smi match: CS(C)~O CS(C)~O
38: smi match: CS(C)(~O)~O CS(C)(~O)~O
38: smi match: CS(N)(~O)~O CS(N)(~O)~O
38: smi match: CS([OH])(~O)~O CS([OH])(~O)~O
38: smi match: COS(C)(~O)~O COS(C)(~O)~O
38: smi match: *S(C)(~O)~O *S(C)(~O)~O
38: smi match: CN(C)C CN(C)C
38: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1
38: smi match: *C(*)=S *C(*)=S
38: smi match: *OC(*)=S *OC(*)=S
38: smi match: * *
38: smi match: C[SH] C[SH]
38: smi match: c[SH] c[SH]
38: smi match: NC(N)=S NC(N)=S
38: smi match: * *
38: smi match: ***** *****
38: smi match: NC(N)=O NC(N)=O
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing sf.net issue 280.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing sf.net issue 285.
38: [06:34:55] done
38: [06:34:55] done
38: [06:34:55] done
38: [06:34:55] done
38: [06:34:55] done
38: [06:34:55] done
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing Github2441: Add RDProps interface to Conformers.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing Issue2510: Pickle Confs as double.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing Github #2465: Negative atom-map numbers cause depickling to fail.
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing loading pickled mols with conformers
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing conformer reading/writing options
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing property reading options
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing property reading options
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing boost::serialization integration
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
81: [06:34:55] Explicit valence for atom # 2 O, 3, is greater than permitted
81: [06:34:55] Explicit valence for atom # 1 O, 3, is greater than permitted
81: [06:34:55] Explicit valence for atom # 1 C, 5, is greater than permitted
81: [06:34:55] sanitize [06:34:55] UNK: [06:34:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
test 99
Start 99: pyChemReactionSanitize
99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testSanitize.py"
99: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap
99: Test timeout computed to be: 1500
test 100
Start 100: testChemTransforms
100: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms
100: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms
100: Test timeout computed to be: 1500
test 101
Start 101: chemTransformsTestCatch
101: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms
101: Test timeout computed to be: 1500
test 102
Start 102: tautomerQueryTestCatch
102: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch
102: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery
102: Test timeout computed to be: 1500
59: smi: ClC1CCCCC1
59: smi: ClC1CCCCC1
59: smi: ClC1CCCCC1Br
59: smi: c1ccccc1
59: smi: c1ccncc1
59: smi: c1cc[nH]c1
59: smi: c1cc[nH]c1
59: smi: c1cc[pH]c1
59: [06:34:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
59: [06:34:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
59: CbC(aC)aC
59: CaC(bC)aC
59: CbC(bC)aC
59: O.C
59: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O
59: [06:34:55] SMILES Parse Error: syntax error while parsing: c%()ccccc%()
59: [06:34:55] SMILES Parse Error: check for mistakes around position 4:
59: [06:34:55] c%()ccccc%()
59: [06:34:55] ~~~^
59: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()'
59: [06:34:55] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000)
59: [06:34:55] SMILES Parse Error: check for mistakes around position 9:
59: [06:34:55] c%(100000)ccccc%(100000)
59: [06:34:55] ~~~~~~~~^
59: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)'
59: [06:34:55] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111'
59: [06:34:55] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1'
59: [06:34:55] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C#
59: [06:34:55] SMILES Parse Error: check for mistakes around position 14:
59: [06:34:55] COc(c1)cccc1C#
59: [06:34:55] ~~~~~~~~~~~~~^
59: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#'
59: [06:34:55] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C#
59: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#'
59: [06:34:55] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C#
59: [06:34:55] SMILES Parse Error: check for mistakes around position 14:
59: [06:34:55] COc(c1)cccc1C#
59: [06:34:55] ~~~~~~~~~~~~~^
59: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#'
59: [06:34:55] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C#
59: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#'
59: [06:34:55] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C#
59: [06:34:55] SMILES Parse Error: check for mistakes around position 14:
59: [06:34:55] COc(c1)cccc1C#
59: [06:34:55] ~~~~~~~~~~~~~^
59: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#'
59: [06:34:55] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C#
59: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#'
63: [06:34:55] w block attempts to set wedging on bond 0 more than once.
63: [06:34:55] improperly formatted w block
63: [06:34:55] atom 3 is not associated with bond 1(1-2) in w block
94: [06:34:55] -------------------------------------
94: [06:34:55] Test Reaction StructuralFingerprint
94: [06:34:55] -------------------------------------
94: [06:34:55] Test Reaction DifferenceFingerprint
61/235 Test #88: v2FileParsersCatchTest ................. Passed 0.08 sec
38: [06:34:55] done
38: [06:34:55] -------------------------------------
38: [06:34:55] Testing github issue 6036
62/235 Test #38: graphmoltestPickler .................... Passed 0.28 sec
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20
81: [06:34:55] skipping block at line 7: 'BEGIN ATOM'
81: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL
81: END
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: no stream
81: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp
81: Failed Expression: dp_inStream
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x000055A227C36774 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 4# 0x000055A227BF1D7D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 5# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 6# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 7# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 13# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: no stream
81: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp
81: Failed Expression: dp_inStream
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x000055A227C36774 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 4# 0x000055A227BF1F58 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 5# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 6# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 7# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 13# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: no stream
81: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp
81: Failed Expression: dp_inStream
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x000055A227C36774 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 4# 0x000055A227BF2391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 5# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 6# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 7# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 13# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: no stream
81: Violation occurred on line 264 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp
81: Failed Expression: dp_inStream
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x000055A227C36774 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 4# 0x000055A227BF2716 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 5# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 6# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 7# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 13# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: no stream
81: Violation occurred on line 577 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp
81: Failed Expression: dp_sInStream != nullptr
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x000055A227C36774 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 4# 0x000055A227BF2993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 5# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 6# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 7# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 13# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 21
81: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 20
81: [06:34:55] BEGIN SGROUP line not found on line 14
81: [06:34:55] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped.
81: [06:34:55] END SGROUP line not found on line 14
81: [06:34:55] END SGROUP line not found on line 14
81: [06:34:55] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring.
81: [06:34:55] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring.
81: [06:34:55]
81:
81: ****
test 103
Start 103: pyTautomerQuery
103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rough_test.py"
103: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap
103: Test timeout computed to be: 1500
59: C=c1s/c2n(c1=O)CCCCCCC\N=2
59: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1
59: [06:34:55] SMILES Parse Error: extra close parentheses while parsing: C)
59: [06:34:55] SMILES Parse Error: check for mistakes around position 2:
59: [06:34:55] C)
59: [06:34:55] ~^
59: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)'
63/235 Test #94: testReactionFingerprints ............... Passed 0.05 sec
64/235 Test #21: testPyGeometry ......................... Passed 0.32 sec
74: [06:34:55] Finished: testMae()
74: [06:34:55] -----------------------------------------
74:
74: [06:34:55]
74: -----------------------------------------
74: [06:34:55] Finished: testTdt()
74: [06:34:55] -----------------------------------------
74:
65/235 Test #74: testGeneralFileReader .................. Passed 0.13 sec
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] WARNING: not removing hydrogen atom without neighbors
84: [06:34:55] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document.
90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110
90: processing
90: launch :0
90: launch :1
90: launch :2
90: launch :3
93: smi: O=C1CNC(=O)CN1
93: 1: O=C1CNC(=O)CN1
93: 2: COOC
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5]
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]'
93: O=C1CNC(=O)CN1
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] mapped atoms in the reactants were not mapped in the products.
93: unmapped numbers are: 4
67: Randomness seeded to: 2045093192
67: ===============================================================================
67: All tests passed (580 assertions in 18 test cases)
67:
73: [06:34:55] Finished: testMolSup()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testRandMolSup()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
71: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
81: Range Error
81: idx
81: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp
81: Failed Expression: 99 < 9
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
81: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# 0x000055A227C3638F in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 7# 0x000055A227BF7D93 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 16# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring.
81: [06:34:55] Multiple ATTCHPT values for atom 2 on line 9
81: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 12
81: [06:34:55] SMARTS Parse Error: syntax error while parsing: [#6;R
81: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R'
81: [06:34:55] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it.
81: [06:34:55] Skipping empty SMARTS value for SMARTSQ.
81: [06:34:55] unrecognized QUERYOP '>' for SMARTSQ. Query ignored.
test 104
Start 104: testSubgraphs1
104: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1
104: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs
104: Test timeout computed to be: 1500
test 105
Start 105: testSubgraphs2
105: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2
105: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs
105: Test timeout computed to be: 1500
test 106
Start 106: subgraphsCatch
106: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch
106: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs
106: Test timeout computed to be: 1500
test 107
Start 107: filterCatalogTest
107: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest
107: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog
107: Test timeout computed to be: 1500
30: ...[06:34:55] Molecule does not have explicit Hs. Consider calling AddHs()
63: [06:34:55]
63:
63: ****
63: Range Error
63: idx
63: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp
63: Failed Expression: 20 < 20
63: ----------
63: Stacktrace:
63: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
63: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
63: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
63: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector<RDKit::Canon::AtomColors, std::allocator<RDKit::Canon::AtomColors> >&, std::vector<unsigned int, std::allocator<unsigned int> > const&, std::vector<RDKit::Canon::MolStackElem, std::allocator<RDKit::Canon::MolStackElem> >&, boost::dynamic_bitset<unsigned long, std::allocator<unsigned long> > const*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector<RDKit::Canon::AtomColors, std::allocator<RDKit::Canon::AtomColors> >&, std::vector<unsigned int, std::allocator<unsigned int> > const&, RDKit::SmilesWriteParams const&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, boost::dynamic_bitset<unsigned long, std::allocator<unsigned long> > const*, boost::dynamic_bitset<unsigned long, std::allocator<unsigned long> > const*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
63: 7# 0x0000557A1480041D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 8# 0x0000557A148516E8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 9# 0x0000557A14852208 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 10# 0x0000557A14852680 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 11# 0x0000557A14823CC3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 12# 0x0000557A1482402C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 13# 0x0000557A147B5CEE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 14# 0x00007EFD57E33CA8 in /lib/x86_64-linux-gnu/libc.so.6
63: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
63: 16# 0x0000557A147B5D31 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: ----------
63: ****
63:
63: [06:34:55]
63:
63: ****
63: Range Error
63: idx
63: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp
63: Failed Expression: 20 < 20
63: ----------
63: Stacktrace:
63: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
63: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
63: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
63: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector<RDKit::Canon::AtomColors, std::allocator<RDKit::Canon::AtomColors> >&, std::vector<unsigned int, std::allocator<unsigned int> > const&, std::vector<RDKit::Canon::MolStackElem, std::allocator<RDKit::Canon::MolStackElem> >&, boost::dynamic_bitset<unsigned long, std::allocator<unsigned long> > const*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector<RDKit::Canon::AtomColors, std::allocator<RDKit::Canon::AtomColors> >&, std::vector<unsigned int, std::allocator<unsigned int> > const&, RDKit::SmilesWriteParams const&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, boost::dynamic_bitset<unsigned long, std::allocator<unsigned long> > const*, boost::dynamic_bitset<unsigned long, std::allocator<unsigned long> > const*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
63: 7# 0x0000557A1480041D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 8# 0x0000557A148516E8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 9# 0x0000557A14852208 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 10# 0x0000557A14852680 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 11# 0x0000557A14823CC3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 12# 0x0000557A1482402C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 13# 0x0000557A147B5CEE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: 14# 0x00007EFD57E33CA8 in /lib/x86_64-linux-gnu/libc.so.6
63: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
63: 16# 0x0000557A147B5D31 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch
63: ----------
63: ****
63:
63: [06:34:55] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5'
63: [06:34:55] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5'
63: [06:34:55] SMARTS Parse Error: syntax error while parsing: C1C)foo
63: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo'
63: [06:34:55] SMILES Parse Error: extra close parentheses while parsing: C1C)foo
63: [06:34:55] SMILES Parse Error: check for mistakes around position 4:
63: [06:34:55] C1C)foo
63: [06:34:55] ~~~^
63: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo'
63: ===============================================================================
63: All tests passed (1584 assertions in 68 test cases)
63:
66/235 Test #59: smiTest1 ............................... Passed 0.21 sec
67/235 Test #67: depictorCatch .......................... Passed 0.17 sec
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
81: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 12
81: [06:34:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
81: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
81: [06:34:55] WARNING: Skipping property bar because the value includes an illegal blank line
81: [06:34:55] WARNING: Skipping property baz because the value includes an illegal blank line
81: [06:34:55] WARNING: Skipping property bletch
81: nope because the name includes a newline
81: [06:34:55] WARNING: Skipping property bletch
81: nope2 because the name includes a newline
81: [06:34:55]
81:
81: ****
81: Post-condition Violation
81: Element 'QQQ' not found
81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h
81: Failed Expression: anum > -1
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x00007FB4CC0C8511 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# 0x00007FB4CC0D3AC2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0D4FAD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227BC947C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Post-condition Violation
81: Element 'QQQ' not found
81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h
81: Failed Expression: anum > -1
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x00007FB4CC0C8511 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# 0x00007FB4CC0D3AC2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0D4FAD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227BC8B5A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Post-condition Violation
81: Element 'QQQ' not found
81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h
81: Failed Expression: anum > -1
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x00007FB4CC0C8511 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# 0x00007FB4CC0D1DEA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0D216D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227BC9424 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Post-condition Violation
81: Element 'QQQ' not found
81: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h
81: Failed Expression: anum > -1
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# 0x00007FB4CC0C8511 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# 0x00007FB4CC0D1DEA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 5# 0x00007FB4CC0D216D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 9# 0x000055A227BC90C2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 13# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 14# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 15# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 16# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 18# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55] atom 3 has a negative isotope value. line: 15
test 108
Start 108: pyFilterCatalog
108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rough_test.py"
108: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap
108: Test timeout computed to be: 1500
test 109
Start 109: testFragCatalog
109: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog
109: Test timeout computed to be: 1500
68/235 Test #63: smiTestCatch ........................... Passed 0.19 sec
93: [06:34:55] atom 0 in product 0 has multiple charge specifications.
93: mass: 15.0001
93: Oc1ccccn1
93: Oc1ccc[nH]1
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2]
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]'
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: ([C:2]
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]'
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2]
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]'
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: [C:2])
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])'
93: [06:34:55] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5]
93: [06:34:55] SMILES Parse Error: check for mistakes around position 2:
93: [06:34:55] [Q:1][C:2][C:3](=[O:4])[O:5]
93: [06:34:55] ~^
93: [06:34:55] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]'
93: [06:34:55] reactant 2 has no mapped atoms.
93: [06:34:55] >> Atoms within one molecule have different RXN roles.
93: [06:34:55] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role.
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2]
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]'
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: ([C:2]
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]'
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: [C:1][C:2])
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])'
93: [06:34:55] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2]
93: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]'
93: [06:34:55] reactant 0 has no mapped atoms.
93: [06:34:55] reactant 1 has no mapped atoms.
93: [06:34:55] reactant 3 has no mapped atoms.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 5 found multiple times.
93: [06:34:55] product atom-mapping number 6 found multiple times.
93: [06:34:55] product atom-mapping number 7 found multiple times.
93: [06:34:55] product atom-mapping number 8 found multiple times.
93: [06:34:55] product atom-mapping number 12 found multiple times.
93: [06:34:55] product atom-mapping number 9 found multiple times.
93: [06:34:55] product atom-mapping number 10 found multiple times.
93: [06:34:55] product atom-mapping number 11 found multiple times.
93: [06:34:55] reactant 0 has no mapped atoms.
93: [06:34:55] reactant 1 has no mapped atoms.
93: [06:34:55] reactant 3 has no mapped atoms.
93: [06:34:55] reactant atom-mapping number 19 found multiple times.
93: [06:34:55] reactant atom-mapping number 25 found multiple times.
93: [06:34:55] reactant atom-mapping number 20 found multiple times.
93: [06:34:55] reactant atom-mapping number 21 found multiple times.
93: [06:34:55] reactant atom-mapping number 22 found multiple times.
93: [06:34:55] reactant atom-mapping number 23 found multiple times.
93: [06:34:55] reactant atom-mapping number 24 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br
93: [06:34:55] product atom-mapping number 5 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 5 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br
93: [06:34:55] product atom-mapping number 5 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 5 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: F[C@](Cl)(Br)O[C@](F)(Cl)Br
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 4 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] mapped atoms in the reactants were not mapped in the products.
93: unmapped numbers are: 4
93: [06:34:55] product atom-mapping number 3 found multiple times.
93: [06:34:55] product atom-mapping number 2 found multiple times.
93: [06:34:55] product atom-mapping number 1 found multiple times.
93: [06:34:55] mapped atoms in the reactants were not mapped in the products.
93: unmapped numbers are: 4
47: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
47: [06:34:55] Explicit valence for atom # 0 Al, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 Al, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 Si, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 Si, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 P, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 P, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 P, 7, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 P, 7, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 As, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 As, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 As, 7, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 As, 7, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 Sb, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 Sb, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 Sb, 7, is greater than permitted
47: [06:34:55] Explicit valence for atom # 0 Sb, 7, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 Bi, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 Bi, 6, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 Bi, 8, is greater than permitted
47: [06:34:55] Explicit valence for atom # 1 Bi, 8, is greater than permitted
47: ===============================================================================
47: All tests passed (4464 assertions in 106 test cases)
47:
69/235 Test #47: graphmolTestsCatch ..................... Passed 0.30 sec
84: [06:34:55] Incomplete atom labelling, cannot make bond
84: [06:34:55] Incomplete atom labelling, cannot make bond
84: [06:34:55] Incomplete atom labelling, cannot make bond
61: Test
61:
61: JDQ443_3d.cxsmi
61:
61: Test
61:
61: JDQ443_atrop1.cxsmi
61:
61: Test
61:
61: JDQ443_atrop2.cxsmi
61:
61: Test
61:
61: JDQ443_atrop3.cxsmi
61:
61: Test
61:
61: JDQ443_atrop4.cxsmi
61:
61: Test
61:
61: JDQ443_atropBad1.cxsmi
61:
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3
100: 1 smi: CC
100: 1 smi: CC
100: 2 smi: CCO[C@H](N)P
100: 2 smi: CC
100: replaceSub smi1:CCP(CC)[C@@H](N)O
100: replaceSub smi1:CCNCC
100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O
100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O
104: -----------------------
104: Subgraph retrieval
104: Finished
104: -----------------------
104: testSubgraphs2a
104: Finished
104: -----------------------
104: testSubgraphs2
105: -----------------------
105: Test1: pathToSubmol
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16
71: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16
81: [06:34:55]
81:
81: ****
81: Invariant Violation
81: bad prop value
81: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp
81: Failed Expression: nSwaps < 2
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# 0x00007FB4CC1947E5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# 0x000055A227C36774 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 5# 0x000055A227C0B43C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 6# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 7# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 12# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 14# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
81: [06:34:55]
81:
81: ****
81: Pre-condition Violation
81: no input stream
81: Violation occurred on line 544 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp
81: Failed Expression: dp_sInStream
81: ----------
81: Stacktrace:
81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
81: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
81: 4# 0x000055A227C0B8C6 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 5# 0x000055A227C7A268 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 6# 0x000055A227C7AD88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 7# 0x000055A227C7B200 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 8# 0x000055A227C4C903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 9# 0x000055A227C4CC6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 10# 0x000055A227BBFCDE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: 11# 0x00007FB4CB633CA8 in /lib/x86_64-linux-gnu/libc.so.6
81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
81: 13# 0x000055A227BBFD21 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest
81: ----------
81: ****
81:
test 110
Start 110: pyFragCatalog
110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/rough_test.py"
110: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap
110: Test timeout computed to be: 1500
test 111
Start 111: testDescriptors
111: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors
111: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
111: Test timeout computed to be: 1500
93: [06:34:55] product atom-mapping number 6 not found in reactants.
93: [06:34:55] product atom-mapping number 7 not found in reactants.
93: [06:34:55] product atom-mapping number 8 not found in reactants.
93: [06:34:55] product atom-mapping number 7 not found in reactants.
93: [06:34:55] product atom-mapping number 8 not found in reactants.
93: [06:34:55] product atom-mapping number 9 not found in reactants.
93: [06:34:55] product atom-mapping number 10 not found in reactants.
93: [06:34:55] mapped atoms in the reactants were not mapped in the products.
93: unmapped numbers are: 6
93: [06:34:55] product atom-mapping number 7 not found in reactants.
93: [06:34:55] product atom-mapping number 8 not found in reactants.
93: [06:34:55] product atom-mapping number 9 not found in reactants.
93: [06:34:55] product atom-mapping number 10 not found in reactants.
93: [06:34:55] mapped atoms in the reactants were not mapped in the products.
93: unmapped numbers are: 6
93: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6]
93: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6]
61: Test
61:
61: RP-6306_atrop1.cxsmi
61:
61: Test
61:
61: RP-6306_atrop2.cxsmi
61:
61: Test
61:
61: RP-6306_atrop3.cxsmi
61:
61: Test
61:
61: RP-6306_atrop4.cxsmi
61:
61: Test
61:
61: RP-6306_atrop5.cxsmi
61:
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
61: Test
61:
61: RP-6306_atrop6.cxsmi
61:
61: Test
61:
61: RP-6306_atropBad1.cxsmi
61:
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5
96: Randomness seeded to: 384643273
96: [06:34:55] atom 0 in product 0 has multiple charge specifications.
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 34
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 36
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 38
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 40
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 42
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 87
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 89
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 91
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 93
96: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 95
96: [06:34:55] mapped atoms in the reactants were not mapped in the products.
96: unmapped numbers are: 2
96: [06:34:55] mapped atoms in the reactants were not mapped in the products.
96: unmapped numbers are: 2
96: [06:34:55] SMARTS Parse Error: unclosed ring for input: 'CC1'
96: [06:34:55] SMILES Parse Error: unclosed ring for input: 'CC1'
96: [06:34:55] mapped atoms in the reactants were not mapped in the products.
96: unmapped numbers are: 2
96: [06:34:55] product atom-mapping number 2 not found in reactants.
96: [06:34:55] mapped atoms in the reactants were not mapped in the products.
96: unmapped numbers are: 2
96: [06:34:55] product atom-mapping number 2 not found in reactants.
106: Randomness seeded to: 1261425307
106: ---------
106: ===============================================================================
106: All tests passed (11 assertions in 1 test case)
106:
73: [06:34:55] Finished: testSmilesSup()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] ------------------------------------------------------
73: [06:34:55] SMILES Parse Error: syntax error while parsing: fail
73: [06:34:55] SMILES Parse Error: check for mistakes around position 1:
73: [06:34:55] fail
73: [06:34:55] ^
73: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail'
73: [06:34:55] ERROR: Smiles parse error on line 3
73: [06:34:55] ERROR: Cannot create molecule from : 'fail'
73: [06:34:55] ------------------------------------------------------
73: [06:34:55] ------------------------------------------------------
73: [06:34:55] >>> This may result in an infinite loop. It should finish almost immediately:
73: [06:34:55] <<< done.
73: [06:34:55] Finished: testSmilesSupFromText()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testSmilesWriter()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
70/235 Test #106: subgraphsCatch ......................... Passed 0.04 sec
test 112
Start 112: testAUTOCORR2D
112: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D
112: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
112: Test timeout computed to be: 1500
61: Test
61:
61: RP-6306_atropBad2.cxsmi
61:
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5
84: [06:34:55] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas
84: [06:34:55] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas
84: [06:34:55] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast
84: [06:34:55] Failed to parse XML fragment 5 node: b attribute: Order: 5
84: [06:34:55] Invalid or missing fragment id from CDXML fragment, assigning new one...
84: ===============================================================================
84: All tests passed (263 assertions in 7 test cases)
84:
105: Finished
105: -----------------------
105: Test2: Atom Environments
105: Finished
105: -----------------------
105: Test 3: Atom Environments (Extension)
105: Finished
105: -----------------------
105: Testing github Issue103: stereochemistry and pathToSubmol
105: Finished
105: -----------------------
105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order)
105: Finished
101: Randomness seeded to: 645588635
101: [06:34:55] Incomplete atom labelling, cannot make bond
101: [06:34:55]
101:
101: ****
101: Invariant Violation
101: molzip: bond info already exists for end atom with label:1
101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp
101: Failed Expression: !bond.b
101: ----------
101: Stacktrace:
101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional<std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 4# 0x0000564612CF71D6 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 5# 0x0000564612D48F28 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 6# 0x0000564612D49A48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 7# 0x0000564612D49EC0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 8# 0x0000564612D1B6C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 9# 0x0000564612D1BA2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 10# 0x0000564612CEB67E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 11# 0x00007F18A9E33CA8 in /lib/x86_64-linux-gnu/libc.so.6
101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
101: 13# 0x0000564612CEB6C1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: ----------
101: ****
101:
41: [06:34:55] sorting (hanoi sort) vectors
96: [06:34:55] CX Extensions: Substance group hierarchy is not always preserved.
96: [06:34:55] CX Extensions: Substance group hierarchy is not always preserved.
100: [06:34:55] SMARTS Parse Error: syntax error while parsing: bar
100: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar'
71/235 Test #84: cdxmlParserCatchTest ................... Passed 0.16 sec
72/235 Test #105: testSubgraphs2 ......................... Passed 0.06 sec
73: [06:34:55] Finished: testSDWriter()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
test 113
Start 113: testATF
113: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF
113: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
113: Test timeout computed to be: 1500
test 114
Start 114: testBCUT
114: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT
114: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
114: Test timeout computed to be: 1500
73: [06:34:55] Finished: testSDSupplierEnding()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testSuppliersEmptyFile()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testCisTrans()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testStereoRound()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
73: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
73: [06:34:55] Finished: testIssue226()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testTDTSupplier1()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
101: [06:34:55] Incomplete atom labelling, cannot make bond
101: [06:34:55]
101:
101: ****
101: Invariant Violation
101: molzip: bond info already exists for end atom with label:1
101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp
101: Failed Expression: !bond.b
101: ----------
101: Stacktrace:
101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional<std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 4# 0x0000564612CF71D6 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 5# 0x0000564612D48F28 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 6# 0x0000564612D49A48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 7# 0x0000564612D49EC0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 8# 0x0000564612D1B6C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 9# 0x0000564612D1BA2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 10# 0x0000564612CEB67E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 11# 0x00007F18A9E33CA8 in /lib/x86_64-linux-gnu/libc.so.6
101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
101: 13# 0x0000564612CEB6C1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: ----------
101: ****
101:
96: [06:34:55] reactant 0 has no mapped atoms.
96: [06:34:55] product 0 has no mapped atoms.
96: [06:34:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
96: [06:34:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
96: [06:34:55] Explicit valence for atom # 1 O, 5, is greater than permitted
96: ===============================================================================
96: All tests passed (722 assertions in 30 test cases)
96:
73: [06:34:55] Finished: testTDTSupplier2()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73/235 Test #96: rxnTestCatch ........................... Passed 0.12 sec
test 115
Start 115: testEEM
115: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM
115: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
115: Test timeout computed to be: 1500
73: [06:34:55] Finished: testTDTSupplier3()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testSDSupplierFromText()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
109: 21
73: [06:34:55] ERROR: Problems encountered parsing data fields
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] ERROR: Problems encountered parsing data fields
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Spurious data before the first property will be ignored
73: [06:34:55] Property <ID> will be truncated after the first blank line
73: [06:34:55] Property <ID> will be truncated after the first blank line
73: [06:34:55] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
73: [06:34:55] Finished: testSDSupplierStrLax1()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] ERROR: Problems encountered parsing data fields
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
73: [06:34:55] Finished: testSDSupplierStrLax2()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] ERROR: Problems encountered parsing data fields
73: [06:34:55] ERROR: moving to the beginning of the next molecule
112: [06:34:55] ----------------------------
112: start test autocorr2D
73: [06:34:55] ERROR: Problems encountered parsing data fields
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Spurious data before the first property will be ignored
73: [06:34:55] Property <ID> will be truncated after the first blank line
73: [06:34:55] Property <ID> will be truncated after the first blank line
73: [06:34:55] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
73: [06:34:55] Finished: testSDSupplierFromTextStrLax1()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] ERROR: Problems encountered parsing data fields
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
73: [06:34:55] Finished: testSDSupplierFromTextStrLax2()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testIssue265()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] ERROR: End of data field name not found
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Explicit valence for atom # 0 F, 2, is greater than permitted
73: [06:34:55] ERROR: Could not sanitize molecule ending on line 16
73: [06:34:55] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted
73: [06:34:55] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] ERROR: Bond line too short: 'M END' on line 18
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Finished: testSDErrorHandling()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
104: Finished
104: -----------------------
104: Path retrieval
104: Finished
104: -----------------------
104: Path retrieval2
104: Finished
104: -----------------------
104: Unique Subgraph retrieval
104: Finished
104: -----------------------
104: testUniqueSubgraphs2
101: [06:34:55] Incomplete atom labelling, cannot make bond
101: [06:34:55]
101:
101: ****
101: Invariant Violation
101: molzip: bond info already exists for end atom with label:1
101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp
101: Failed Expression: !bond.b
101: ----------
101: Stacktrace:
101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional<std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 4# 0x0000564612CF71D6 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 5# 0x0000564612D48F28 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 6# 0x0000564612D49A48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 7# 0x0000564612D49EC0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 8# 0x0000564612D1B6C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 9# 0x0000564612D1BA2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 10# 0x0000564612CEB67E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 11# 0x00007F18A9E33CA8 in /lib/x86_64-linux-gnu/libc.so.6
101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
101: 13# 0x0000564612CEB6C1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: ----------
101: ****
101:
93: [06:34:55] mapped atoms in the reactants were not mapped in the products.
93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16
73: [06:34:55] Finished: testIssue381()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
111: [06:34:55] -------------------------------------
111: [06:34:55] Test Crippen parameter acquisition.
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test Crippen calculation.
73: [06:34:55] Finished: testSetStreamIndices()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
61: Test
61:
61: RP-6306_3d.cxsmi
61:
61: Test
61:
61: Sotorasib_atrop1.cxsmi
61:
61: Test
61:
61: Sotorasib_atrop2.cxsmi
61:
61: Test
61:
61: Sotorasib_atrop3.cxsmi
61:
61: Test
61:
61: Sotorasib_atrop4.cxsmi
61:
61: Test
61:
61: Sotorasib_atrop5.cxsmi
61:
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
81: [06:34:55] ERROR: molecules without atoms cannot be exported to Maestro files.
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
81: [06:34:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
73: [06:34:55] Finished: testMixIterAndRandom()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
81: [06:34:55] ERROR: the mol cannot be kekulized, and will not be written to the output file.
81: [06:34:55] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file.
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
73: build:
73: [06:34:55] Finished: testRemoveHs()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
101: [06:34:55] Incomplete atom labelling, cannot make bond
101: [06:34:55] Incomplete atom labelling, cannot make bond
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
61: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored
101: [06:34:55] Incomplete atom labelling, cannot make bond
101: [06:34:55]
101:
101: ****
101: Invariant Violation
101: molzip: bond info already exists for end atom with label:1
101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp
101: Failed Expression: !bond.b
101: ----------
101: Stacktrace:
101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional<std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 4# 0x0000564612CF71D6 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 5# 0x0000564612D48F28 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 6# 0x0000564612D49A48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 7# 0x0000564612D49EC0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 8# 0x0000564612D1B6C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 9# 0x0000564612D1BA2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 10# 0x0000564612CEB67E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 11# 0x00007F18A9E33CA8 in /lib/x86_64-linux-gnu/libc.so.6
101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
101: 13# 0x0000564612CEB6C1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: ----------
81: [06:34:55] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[06:34:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
81: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
81: [06:34:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
81: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
61: Test
61:
61: Sotorasib_atropBad1.cxsmi
61:
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14
114: [06:34:55] -------------------------------------
114: [06:34:55] Basic BCUT tests.
95: 30000000 30000000
74/235 Test #100: testChemTransforms ..................... Passed 0.12 sec
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14
73: [06:34:55] Finished: testGetItemText()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
test 116
Start 116: testPBF
116: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF
116: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
116: Test timeout computed to be: 1500
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14
61: Test
61:
61: Sotorasib_atropBad2.cxsmi
61:
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14
101: ****
101:
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test Issue262: problems with Crippen calculation from pickles.
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test AMW calculation.
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test Exact MW calculation.
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test Labute ASA descriptors.
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test TPSA descriptors.
115: =>start test EEM
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: 0
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
75/235 Test #113: testATF ................................ Passed 0.05 sec
61: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
93: [06:34:55] product atom-mapping number 17 not found in reactants.
93: [06:34:55] product atom-mapping number 18 not found in reactants.
93: [06:34:55] mapped atoms in the reactants were not mapped in the products.
93: unmapped numbers are: 12
test 117
Start 117: testRDFcustom
117: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom
117: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
117: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
71: Atropisomers- 1 hits 3 misses
71: Final results:
71: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses
73: [06:34:55] Finished: testForwardSDSupplier()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testMissingCRSDSupplier()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testIssue3482695()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
76/235 Test #71: testAtropisomers ....................... Passed 0.26 sec
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
test 118
Start 118: testRDF
118: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF
118: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
118: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
73: [06:34:55] ERROR: Cannot convert 'foo' to unsigned int on line 557
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Finished: testIssue3525673()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testBlankLinesInProps()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testSkipLines()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testGitHub23()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testGitHub88()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
101: [06:34:55] Incomplete atom labelling, cannot make bond
101: [06:34:55]
101:
101: ****
101: Invariant Violation
101: molzip: bond info already exists for end atom with label:1
101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp
101: Failed Expression: !bond.b
101: ----------
101: Stacktrace:
101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional<std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 4# 0x0000564612CF71D6 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 5# 0x0000564612D48F28 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 6# 0x0000564612D49A48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 7# 0x0000564612D49EC0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 8# 0x0000564612D1B6C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 9# 0x0000564612D1BA2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 10# 0x0000564612CEB67E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 11# 0x00007F18A9E33CA8 in /lib/x86_64-linux-gnu/libc.so.6
101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
101: 13# 0x0000564612CEB6C1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: ----------
101: ****
101:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
101: [06:34:55]
101:
101: ****
101: Invariant Violation
101: molzip: zipped Bond already exists, perhaps labels are duplicated
101: Violation occurred on line 735 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp
101: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx())
101: ----------
101: Stacktrace:
101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional<std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1
101: 5# 0x0000564612CEC47D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 6# 0x0000564612D48F28 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 7# 0x0000564612D49A48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 8# 0x0000564612D49EC0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 9# 0x0000564612D1B6C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 10# 0x0000564612D1BA2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 11# 0x0000564612CEB67E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: 12# 0x00007F18A9E33CA8 in /lib/x86_64-linux-gnu/libc.so.6
101: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
101: 14# 0x0000564612CEB6C1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch
101: ----------
101: ****
101:
101: ===============================================================================
101: All tests passed (674 assertions in 9 test cases)
101:
114: [06:34:55] done
114: [06:34:55] -------------------------------------
114: [06:34:55] Larger BCUT tests.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
77/235 Test #101: chemTransformsTestCatch ................ Passed 0.16 sec
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
73: [06:34:55] Finished: testGitHub2285()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] SMILES Parse Error: unclosed ring for input: 'c1ccccc'
73: [06:34:55] ERROR: Smiles parse error on line 1
73: [06:34:55] ERROR: Cannot create molecule from : 'c1ccccc'
73: [06:34:55] SMILES Parse Error: extra open parentheses while parsing: C(C
73: [06:34:55] SMILES Parse Error: check for mistakes around position 2:
73: [06:34:55] C(C
73: [06:34:55] ~^
73: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C'
73: [06:34:55] ERROR: Smiles parse error on line 3
73: [06:34:55] ERROR: Cannot create molecule from : 'C(C'
73: [06:34:55] Explicit valence for atom # 1 C, 5, is greater than permitted
73: [06:34:55] ERROR: Could not sanitize molecule on line 5
73: [06:34:55] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted
73: [06:34:55] Explicit valence for atom # 1 F, 2, is greater than permitted
73: [06:34:55] ERROR: Could not sanitize molecule ending on line 21
73: [06:34:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
73: [06:34:55] Explicit valence for atom # 1 F, 2, is greater than permitted
73: [06:34:55] ERROR: Could not sanitize molecule ending on line 21
73: [06:34:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
73: [06:34:55] Explicit valence for atom # 1 F, 2, is greater than permitted
test 119
Start 119: testMORSE
119: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE
119: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
119: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
73: [06:34:55] ERROR: Could not sanitize molecule ending on line 21
73: [06:34:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
73: [06:34:55] ERROR: Atom line too short: ' -9.6' on line 28
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Explicit valence for atom # 1 F, 2, is greater than permitted
73: [06:34:55] ERROR: Could not sanitize molecule ending on line 21
73: [06:34:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
73: [06:34:55] ERROR: Atom line too short: ' -9.6' on line 28
73: [06:34:55] ERROR: moving to the beginning of the next molecule
73: [06:34:55] Finished: testGitHub2479()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55]
73:
73: ****
73: Invariant Violation
73: bad chiral bond
73: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp
73: Failed Expression: bnd
73: ----------
73: Stacktrace:
73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
73: 2# 0x00007FFA5C394DAD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
73: 4# 0x00005586306A57CE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier
73: 5# 0x00005586306A470B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier
73: 6# 0x00007FFA5B833CA8 in /lib/x86_64-linux-gnu/libc.so.6
73: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
73: 8# 0x00005586306A4981 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier
73: ----------
73: ****
73:
73: [06:34:55] Finished: testGitHub2881()
73: [06:34:55] -----------------------------------------
73:
73: [06:34:55] -----------------------------------------
73: [06:34:55] Finished: testGitHub3517()
73: [06:34:55] -----------------------------------------
73:
78/235 Test #73: testMolSupplier ........................ Passed 0.28 sec
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
116: [06:34:55] -------------------------------------
116: [06:34:55] Basic PBF tests.
test 120
Start 120: test3D
120: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D
120: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
120: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
107: Warning: molecule failed filter
107: Warning: molecule failed filter: reason hzone_phenol_A(479)
107: v = {
107: 0,23},
107: 1,22},
107: 2,20},
107: 3,19},
107: 4,25},
107: 5,24},
107: 6,18},
107: 7,17},
107: 8,16},
107: 9,21},
107: }
107: match = {
107: 0,23},
107: 1,22},
107: 2,20},
107: 3,19},
107: 4,25},
107: 5,24},
107: 6,18},
107: 7,17},
107: 8,16},
107: 9,21},
107: }
107: Warning: molecule failed filter
107: Warning: molecule failed filter: reason cyano_imine_B(17)
107: v = {
107: 0,11},
107: 1,12},
107: 2,13},
107: 3,14},
107: 4,15},
107: 5,10},
107: 6,9},
107: 7,8},
107: 8,7},
107: 9,6},
107: 10,5},
107: 11,17},
107: 12,16},
107: }
107: match = {
107: 0,11},
107: 1,12},
107: 2,13},
107: 3,14},
107: 4,15},
107: 5,10},
107: 6,9},
107: 7,8},
107: 8,7},
107: 9,6},
107: 10,5},
107: 11,17},
107: 12,16},
107: }
107: Warning: molecule failed filter
61: Test
61:
61: Sotorasib_3d.cxsmi
61:
61: Test
61:
61: ZM374979_atrop1.cxsmi
61:
61: Test
61:
61: ZM374979_atrop2.cxsmi
61:
61: Test
61:
61: ZM374979_atrop3.cxsmi
61:
61: Test
61:
61: ZM374979_atrop4.cxsmi
61:
61: Test
61:
61: ZM374979_atropBad1.cxsmi
61:
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
107: Warning: molecule failed filter: reason keto_keto_gamma(5)
107: v = {
107: 0,0},
107: 1,1},
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
107: 2,2},
107: 3,4},
107: 4,5},
107: 5,6},
107: 6,7},
107: 7,8},
107: 8,9},
107: 9,14},
107: 10,15},
107: 11,16},
107: }
107: match = {
107: 0,0},
107: 1,1},
107: 2,2},
107: 3,4},
107: 4,5},
107: 5,6},
107: 6,7},
107: 7,8},
107: 8,9},
107: 9,14},
107: 10,15},
107: 11,16},
107: }
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
66: [06:34:55] Warning: stereochemistry around double bond may be incorrect in depiction.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
76: [06:34:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110
90: processing2
90: launch2 :0
90: launch2 :1
90: launch2 :2
90: launch2 :3
76: 0.40201265 0.40201265
76: -0.13299436 -0.13299436
76: 1.00000017 1.00000017
76: 0.8762226 0.8762226
76: 0.9973909 0.9973909
76: 1.00000003 1.00000003
76: 0.36613799 0.36613799
76: 2.1107185 2.1107185
76: 0.99999982 0.99999982
76: 2.48696157 2.48696157
76: 1.00479935 1.00479935
76: 0.99999999 0.99999999
76: 3.03311841 3.03311841
76: 2.23739955 2.23739955
76: 1.0000001 1.0000001
76: 3.00772337 3.00772337
76: 0.37399294 0.37399294
76: 2.07713325 2.07713325
76: 3.0077234 3.0077234
76: 0.37399312 0.37399312
76: -0.07713336 -0.07713336
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
76: [06:34:55] bond with order 0 found on line 11. This is not part of the MDL specification.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
76: [06:34:55] bond with order 0 found on line 16. This is not part of the MDL specification.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
120: [06:34:55] -------------------------------------
120: [06:34:55] Basic PMI tests.
93: [06:34:55] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs)
93: [06:34:55] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs)
93:
93: [06:34:55] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels
93: -------------
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test Lipinski parameters.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
93: CCOc1ccccc1
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: done
90: preprocessing 3
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110
90: processing3
90: launch3 :0
90: launch3 :1
90: launch3 :2
90: launch3 :3
79/235 Test #76: testMolWriter .......................... Passed 0.33 sec
test 121
Start 121: testWHIM
121: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM
121: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
121: Test timeout computed to be: 1500
89: Randomness seeded to: 1261938440
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
102: Randomness seeded to: 3593014216
102: ===============================================================================
102: All tests passed (93 assertions in 13 test cases)
102:
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
61: Test
61:
61: Mrtx1719_3d.cxsmi
61:
61: Test
61:
61: Mrtx1719_atrop1.cxsmi
61:
61: Test
61:
61: Mrtx1719_atrop2.cxsmi
61:
61: Test
61:
61: Mrtx1719_atrop3.cxsmi
61:
61: Test
61:
61: Mrtx1719_atrop4.cxsmi
61:
61: Test
61:
61: Mrtx1719_atropBad1.cxsmi
61:
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
80/235 Test #102: tautomerQueryTestCatch ................. Passed 0.22 sec
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
test 122
Start 122: testGETAWAY
122: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY
122: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
122: Test timeout computed to be: 1500
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12
61: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
89: [06:34:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that.
115: 100
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
81/235 Test #66: testDepictor ........................... Passed 0.40 sec
test 123
Start 123: testAUTOCORR3D
123: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D
123: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
123: Test timeout computed to be: 1500
30: ......[06:34:55] Molecule does not have explicit Hs. Consider calling AddHs()
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: badWedgeError.sdf
69:
69: Test
69:
69: CrossedDoubleBondWithChiralNbr2.sdf
69:
69: Test
69:
69: CrossedDoubleBondWithChiralNbr.sdf
69:
69: Test
69:
69: SimpleWiggleDoubleBond.sdf
69:
69: Test
69:
69: lostStereoAnd.sdf
69:
69: Test
69:
69: DoubleBondChain.sdf
69:
69: Test
69:
69: UnitsError.sdf
69:
69: Test
69:
69: StarAtom.sdf
69:
69: Test
69:
69: nonProprietary.mol
69:
69: Test
69:
69: ChiralTest.sdf
69:
69: Test
69:
69: TestBond1.mol
69:
69: Test
69:
69: Sgroup_MUL_ParentInMiddle.sdf
69:
69: Test
69:
69: BadRxn.rxn
69:
69: Test
69:
69: FalseChiral.mrv
69:
69: Test
69:
69: FalseChiral.mrv
69:
69: Test
69:
69: Cubane.mrv
69:
69: Test
69:
69: NewChiralTest.mrv
69:
69: Test
69:
69: NewChiralTest.mrv
69:
69: Test
69:
69: NewChiralTestNoChiral.mrv
69:
69: Test
69:
69: NewChiralTestNoChiral.mrv
69:
69: Test
69:
69: NewChiralTestAllChiral.mrv
69:
69: Test
69:
69: NewChiralTestAllChiral.mrv
69:
69: Test
69:
69: DataSgroupMissingUnitsDisplayed.mrv
69:
69: Test
69:
69: lostStereoAnd.mrv
69:
69: Test
69:
69: DoubleBondChain.mrv
69:
69: Test
69:
69: WigglyAndCrossed.mrv
69:
69: Test
69:
69: BondTypes.mrv
69:
69: Test
69:
69: EmbeddedSGroupSUP_MUL.mrv
69:
69: Test
69:
69: EmbeddedSgroupCOP_SUP.mrv
69:
69: Test
69:
69: EmbeddedSgroupDAT_SUP.mrv
69:
69: Test
69:
69: EmbeddedSgroupMULTICENTER_SUP.mrv
69:
69: Test
69:
69: EmbeddedSgroupMUL_MUL.mrv
69:
69: Test
69:
69: EmbeddedSgroupMUL_MUL2.mrv
69:
69: Test
69:
69: EmbeddedSgroupMUL_SUP.mrv
69:
69: Test
69:
69: EmbeddedSgroupSRU_SUP.mrv
69:
69: Test
69:
69: EmbeddedSgroupSUPEXP_SUP.mrv
69:
69: Test
69:
69: EmbeddedSgroupSUPEXP_SUP2.mrv
69:
69: Test
69:
69: EmbeddedSgroupSUP_MULTICENTER.mrv
69:
69: Test
69:
69: EmbeddedSgroupSUP_SUP.mrv
69:
69: Test
69:
69: EmbeddedSgroupSUP_SUP2.mrv
69:
69: Test
69:
69: RgroupBad.mrv
69:
69: Test
69:
69: valenceLessThanDrawn.mrv
69:
69: Test
69:
69: data_sgroup_no_fieldname.mrv
69:
69: Test
69:
69: data_sgroup_empty_field_data.mrv
69:
69: Test
69:
69: radical_value.mrv
69:
69: Test
69:
69: emptyOneLineAtomList.mrv
69:
69: Test
69:
69: mrvValence_value.mrv
69:
69: Test
69:
69: ChiralTest2.mrv
69:
69: Test
69:
69: ChiralTest.mrv
69:
69: Test
69:
69: SnCl2.mrv
69:
69: Test
69:
69: SnH2Cl2.mrv
69:
69: Test
69:
69: marvin01.mrv
69:
69: Test
69:
69: marvin02.mrv
69:
69: Test
69:
69: marvin07.mrv
69:
69: Test
69:
69: marvin10.mrv
69:
69: Test
69:
69: marvin06.mrv
69:
69: Test
69:
69: marvin12.mrv
69:
69: Test
69:
69: EmptyMol.mrv
69:
69: Test
69:
69: Sparse.mrv
69:
69: Test
69:
69: Sparse2.mrv
69:
69: Test
69:
69: Sparse3.mrv
69:
69: Test
69:
69: MarvinNoCoords.mrv
69:
69: Test
69:
69: aspirin.mrv
69:
69: Test
69:
69: MarvinStereoGroupsZeros.mrv
69:
69: Test
69:
69: MarvinStereoGroupsAbs.mrv
69:
69: Test
69:
69: triphenylphosphine.mrv
69:
69: Test
69:
69: MarvinOldSuperGroupTest.mrv
69:
69: Test
69:
69: RadicalTests.mrv
69:
69: Test
69:
69: AnyBond.mrv
69:
69: Test
69:
69: cisBenzene.mrv
69:
69: Test
69:
69: DativeBond.mrv
69:
69: Test
69:
69: MultipleSgroup.mrv
69:
69: Test
69:
69: SgroupExpanded.mrv
69:
69: Test
69:
69: SgroupMultAttach.mrv
69:
69: Test
69:
69: MarvinMissingX2.mrv
69:
69: Test
69:
69: MarvinMissingY2.mrv
69:
69: Test
69:
69: DataSgroup.mrv
69:
69: Test
69:
69: MulticenterSgroup.mrv
69:
69: [06:34:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10
69: [06:34:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
98: [06:34:55] == testCartesianProduct
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
104: Finished
104: -----------------------
104: testRootedSubgraphs
104: Finished
104: -----------------------
104: testRootedPaths
104: Finished
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
82/235 Test #104: testSubgraphs1 ......................... Passed 0.28 sec
test 124
Start 124: testCoulombMat
124: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat
124: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
124: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: GenericSgroup.mrv
69:
69: Test
69:
69: MonomerSgroup.mrv
69:
69: Test
69:
69: modification_sgroup.mrv
69:
69: Test
69:
69: copolymer_sgroup.mrv
69:
69: Test
69:
69: MultipleSgroupParentInMiddleOfAtomBlock.mrv
69:
69: Test
69:
69: EmbeddedSgroups.mrv
69:
69: Test
69:
69: marvin03.mrv
69:
69: Test
69:
69: MarvinBadMissingMolID.mrv
69:
69: [06:34:55]
69:
69: ****
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test Assert
69: Expression Failed:
69: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp
69: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr
69: ----------
69: Stacktrace:
69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
69: 2# 0x000055A12B89699F in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol
69: 3# 0x000055A12B8A169C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol
69: 4# 0x000055A12B88EA5D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol
69: 5# 0x00007FDC73633CA8 in /lib/x86_64-linux-gnu/libc.so.6
69: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
69: 7# 0x000055A12B88EBE1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol
69: ----------
69: ****
69:
69: Test
69:
69: MarvinBadMissingAtomID.mrv
69:
69: Expected id, elementType for an atom definition in MRV file
98: .[06:34:55] == testEnumerateLibrary
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: MarvinBadX2.mrv
69:
69: The values x2 and y2 must be large floats in MRV file
69: Test
69:
69: MarvinBadY2.mrv
69:
69: The values x2 and y2 must be large floats in MRV file
69: Test
69:
69: MarvinBadStereoGroupsAbs.mrv
69:
69: Unrecognized group definition
103: .....
103: ----------------------------------------------------------------------
103: Ran 5 tests in 0.043s
103:
103: OK
69: Test
69:
69: MarvinBadElementType.mrv
69:
69: Test
69:
69: MarvinBadMissingBondID.mrv
69:
69: Test
69:
69: MarvinBadMissingBondAtomRefs
69:
69: Test
69:
69: MarvinBadMissingBondOrder.mrv
69:
69: bond must have one of: order, queryType, or convention in MRV File
69: Test
69:
69: MarvinBadMissingSruMolID.mrv
69:
69: Expected a molID in MRV file
91: Randomness seeded to: 2299924809
91: ===============================================================================
91: All tests passed (242 assertions in 12 test cases)
91:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: MarvinBadMissingSruID.mrv
69:
69: Test
69:
69: MarvinBadMissingSruRole.mrv
69:
69: Test
69:
69: MarvinBadMissingSruAtomRef.mrv
69:
69: Test
69:
69: MarvinBadMissingSruTitle.mrv
69:
69: Test
69:
69: MarvinBadSruAtomRef.mrv
69:
69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent
69: Test
69:
69: MarvinBadSruID.mrv
69:
69: Test
69:
69: MarvinBadSruRole.mrv
69:
69: Test
69:
69: MarvinBadSruAtomRef.mrv
69:
69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent
98: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/enumeration.pickle'>
98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read())
98: ResourceWarning: Enable tracemalloc to get the object allocation traceback
69: Test
69:
69: MarvinBadSruAtomRef.mrv
69:
69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent
69: Test
69:
69: MarvinBadSruConnect.mrv
69:
69: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: MarvinBadSupAttachAtom.mrv
69:
69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: MarvinBadSupAttachBond.mrv
69:
69: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file
69: Test
69:
69: MarvinBadSupAttachOrder.mrv
69:
69: Order for an AttachmentPoint definition must be an integer in MRV file
69: Test
69:
69: MarvinBadSupAttachAtom.mrv
69:
69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
124: ===================== Testing CoulombMat =======================
69: Test
69:
69: MarvinBadSupAttachAtom.mrv
69:
69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: MarvinBadSupAttachAtom.mrv
69:
69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file
83/235 Test #91: substructTestCatch ..................... Passed 0.38 sec
test 125
Start 125: descriptorsTestCatch
125: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch
125: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors
125: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: MarvinBadSupMissingAttachBond.mrv
69:
69: No attachment point found for bond to the condensed atom in a superatomSgroup
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: MarvinBadSupMissingAttachOrder.mrv
69:
69: Expected atom, order and bond, for an AttachmentPoint definition in MRV file
124: CM test 1 mat Done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
84/235 Test #124: testCoulombMat ......................... Passed 0.03 sec
97: ...[06:34:55]
97:
97: ****
test 126
Start 126: pyMolDescriptors
126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py"
126: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap
126: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: Pre-condition Violation
97: getNumImplicitHs() called without preceding call to calcImplicitValence()
97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp
97: Failed Expression: d_implicitValence > -1
97: ----------
97: Stacktrace:
97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 4# Queries::EqualityQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
97: 5# Queries::AndQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 6# Queries::AndQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 7# Queries::OrQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 9# boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 10# bool boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll<std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(unsigned int*, unsigned int*, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 11# bool boost::vf2_all<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS>, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const&, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector<int, std::allocator<int> >&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, RDKit::SubstructMatchParameters const&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query<int, RDKit::Atom const*, true>*, RDKit::SubstructMatchParameters const&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query<int, RDKit::Atom const*, true>*, RDKit::SubstructMatchParameters const&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query<int, RDKit::Atom const*, true>*, RDKit::SubstructMatchParameters const&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query<int, RDKit::Atom const*, true>*, RDKit::SubstructMatchParameters const&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1
97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > > const&, RDKit::ChemicalReaction const&, std::vector<std::vector<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >, std::allocator<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > > >, std::allocator<std::vector<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >, std::allocator<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1
97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1
97: 21# RDKit::ChemicalReaction::runReactants(std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1
97: 22# _object* RDKit::RunReactants<boost::python::tuple>(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
97: 23# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<_object* (*)(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int), boost::python::default_call_policies, boost::mpl::vector4<_object*, RDKit::ChemicalReaction*, boost::python::tuple, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 25# 0x00007F657912162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 26# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 27# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
97: 28# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
97: 29# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
97: 30# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
97: 31# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
97: 32# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
97: 33# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
97: 34# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
97: 35# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 36# 0x00007F6576DB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 37# 0x00007F6576DB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 38# 0x00007F6576DB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 39# 0x00007F6576DB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 40# 0x00007F6576DB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 41# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
97: 42# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
97: 43# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
97: 44# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
97: 45# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 46# 0x00007F657911E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 47# _PyObject_MakeTpCall in /usr/bin/python3
97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 49# 0x00000000005BEE79 in /usr/bin/python3
97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 51# 0x0000000000547080 in /usr/bin/python3
97: 52# 0x00000000006AB720 in /usr/bin/python3
97: 53# _PyObject_MakeTpCall in /usr/bin/python3
97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 55# 0x00000000005BEE79 in /usr/bin/python3
97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 57# 0x0000000000547080 in /usr/bin/python3
97: 58# 0x00000000006AB720 in /usr/bin/python3
97: 59# _PyObject_MakeTpCall in /usr/bin/python3
97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 61# 0x00000000005BEE79 in /usr/bin/python3
97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 63# 0x0000000000547080 in /usr/bin/python3
97: 64# 0x00000000006AB720 in /usr/bin/python3
97: 65# _PyObject_MakeTpCall in /usr/bin/python3
97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 67# 0x0000000000595987 in /usr/bin/python3
97: 68# _PyObject_MakeTpCall in /usr/bin/python3
97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 70# PyEval_EvalCode in /usr/bin/python3
97: 71# 0x000000000066A861 in /usr/bin/python3
97: 72# 0x000000000066670C in /usr/bin/python3
97: 73# 0x000000000067F713 in /usr/bin/python3
97: 74# 0x000000000067ECE3 in /usr/bin/python3
97: 75# 0x000000000067EB1E in /usr/bin/python3
97: 76# Py_RunMain in /usr/bin/python3
97: 77# Py_BytesMain in /usr/bin/python3
97: 78# 0x00007F6579B26CA8 in /lib/x86_64-linux-gnu/libc.so.6
97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
97: 80# _start in /usr/bin/python3
97: ----------
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: ****
97:
97: [06:34:55]
97:
97: ****
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: Pre-condition Violation
97: getNumImplicitHs() called without preceding call to calcImplicitValence()
97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp
97: Failed Expression: d_implicitValence > -1
97: ----------
97: Stacktrace:
97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 4# Queries::EqualityQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
97: 5# Queries::AndQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 6# Queries::AndQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 7# Queries::OrQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 9# boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 10# bool boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll<std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(unsigned int*, unsigned int*, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 11# bool boost::vf2_all<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS>, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const&, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector<int, std::allocator<int> >&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, RDKit::SubstructMatchParameters const&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query<int, RDKit::Atom const*, true>*, RDKit::SubstructMatchParameters const&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query<int, RDKit::Atom const*, true>*, RDKit::SubstructMatchParameters const&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query<int, RDKit::Atom const*, true>*, RDKit::SubstructMatchParameters const&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query<int, RDKit::Atom const*, true>*, RDKit::SubstructMatchParameters const&, std::map<unsigned int, Queries::Query<int, RDKit::Atom const*, true>*, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, Queries::Query<int, RDKit::Atom const*, true>*> > >&, std::vector<RDKit::RecursiveStructureQuery*, std::allocator<RDKit::RecursiveStructureQuery*> >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1
97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > > const&, RDKit::ChemicalReaction const&, std::vector<std::vector<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >, std::allocator<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > > >, std::allocator<std::vector<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >, std::allocator<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1
97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1
97: 21# RDKit::ChemicalReaction::runReactants(std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1
97: 22# _object* RDKit::RunReactants<boost::python::tuple>(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
97: 23# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<_object* (*)(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int), boost::python::default_call_policies, boost::mpl::vector4<_object*, RDKit::ChemicalReaction*, boost::python::tuple, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 25# 0x00007F657912162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 26# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 27# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
97: 28# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
97: 29# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
97: 30# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
97: 31# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
97: 32# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
97: 33# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
97: 34# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
97: 35# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 36# 0x00007F6576DB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 37# 0x00007F6576DB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 38# 0x00007F6576DB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 39# 0x00007F6576DB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 40# 0x00007F6576DB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
97: 41# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
97: 42# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
97: 43# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
97: 44# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
97: 45# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 46# 0x00007F657911E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
97: 47# _PyObject_MakeTpCall in /usr/bin/python3
97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 49# 0x00000000005BEE79 in /usr/bin/python3
97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 51# 0x0000000000547080 in /usr/bin/python3
97: 52# 0x00000000006AB720 in /usr/bin/python3
97: 53# _PyObject_MakeTpCall in /usr/bin/python3
97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 55# 0x00000000005BEE79 in /usr/bin/python3
97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 57# 0x0000000000547080 in /usr/bin/python3
97: 58# 0x00000000006AB720 in /usr/bin/python3
97: 59# _PyObject_MakeTpCall in /usr/bin/python3
97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 61# 0x00000000005BEE79 in /usr/bin/python3
97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 63# 0x0000000000547080 in /usr/bin/python3
97: 64# 0x00000000006AB720 in /usr/bin/python3
97: 65# _PyObject_MakeTpCall in /usr/bin/python3
97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 67# 0x0000000000595987 in /usr/bin/python3
97: 68# _PyObject_MakeTpCall in /usr/bin/python3
97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3
97: 70# PyEval_EvalCode in /usr/bin/python3
97: 71# 0x000000000066A861 in /usr/bin/python3
97: 72# 0x000000000066670C in /usr/bin/python3
97: 73# 0x000000000067F713 in /usr/bin/python3
97: 74# 0x000000000067ECE3 in /usr/bin/python3
97: 75# 0x000000000067EB1E in /usr/bin/python3
97: 76# Py_RunMain in /usr/bin/python3
97: 77# Py_BytesMain in /usr/bin/python3
97: 78# 0x00007F6579B26CA8 in /lib/x86_64-linux-gnu/libc.so.6
97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
97: 80# _start in /usr/bin/python3
97: ----------
97: ****
97:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
85/235 Test #103: pyTautomerQuery ........................ Passed 0.34 sec
test 127
Start 127: pyMolDescriptors3D
127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/test3D.py"
127: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap
127: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: .........[06:34:55] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
97: [06:34:55] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
97: [06:34:55] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
97: [06:34:55] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
97: .[06:34:55] product atom-mapping number 1 found multiple times.
97: [06:34:55] product atom-mapping number 1 found multiple times.
98: ..[06:34:55] == testRGroupState
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
108: <frozen importlib._bootstrap>:488: RuntimeWarning: to-Python converter for boost::shared_ptr<RDKit::FilterHierarchyMatcher> already registered; second conversion method ignored.
108: <frozen importlib._bootstrap>:488: RuntimeWarning: to-Python converter for boost::shared_ptr<RDKit::FilterCatalogEntry> already registered; second conversion method ignored.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
98: .[06:34:55] == testRandomEnumerateAllBBsLibrary
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
98: ** [1, 1]
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
98: ** [0, 2]
98: ** [1, 0]
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: ................[06:34:55] mapped atoms in the reactants were not mapped in the products.
97: unmapped numbers are: 3
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: [06:34:55] mapped atoms in the reactants were not mapped in the products.
97: unmapped numbers are: 3
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test VSA descriptors.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
111: [06:34:55] done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
111: [06:34:55] -------------------------------------
111: [06:34:55] Test molecular formula calculation.
97: .<frozen importlib._bootstrap>:488: RuntimeWarning: to-Python converter for boost::shared_ptr<RDKit::FilterHierarchyMatcher> already registered; second conversion method ignored.
97: <frozen importlib._bootstrap>:488: RuntimeWarning: to-Python converter for boost::shared_ptr<RDKit::FilterCatalogEntry> already registered; second conversion method ignored.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test Issue 3415534.
111: [06:34:55] done
111: [06:34:55] -------------------------------------
111: [06:34:55] Test Issue3433771: Bad definition for Crippen atom type O11.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
111: [06:34:55] done
98: .[06:34:55] == testRandomEnumerateLibrary
111: [06:34:55] -------------------------------------
111: [06:34:55] Test multithreading
111: reading molecules
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: [06:34:55] done
90: [06:34:55] -------------------------------------
90: [06:34:55] Test GitHub issue 15
90: [06:34:55] done
90: [06:34:55] -------------------------------------
90: [06:34:55] Test GitHub issue 409
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: [06:34:55] mapped atoms in the reactants were not mapped in the products.
97: unmapped numbers are: 3
90: [06:34:55] done
90: [06:34:55] -------------------------------------
90: [06:34:55] Test chiral matching
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: [06:34:55] done
90: [06:34:55] -------------------------------------
90: [06:34:55] Test GitHub issue 688: partially specified chiral substructure queries don't work properly
90: [06:34:55] done
90: [06:34:55] -------------------------------------
90: [06:34:55] Test dative-bond matching
90: [06:34:55] done
90: [06:34:55] -------------------------------------
90: [06:34:55] Test cis/trans matching
90: [06:34:55] done
90: [06:34:55] -------------------------------------
90: [06:34:55] Test cis/trans matching part 2
90: [06:34:55] done
90: [06:34:55] -------------------------------------
90: [06:34:55] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS
90: [06:34:55] done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: 200
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: ..[06:34:55] reactant 2 has no mapped atoms.
97: [06:34:55] reactant 2 has no mapped atoms.
97: [06:34:55] product 1 has no mapped atoms.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: [06:34:55] -------------------------------------
90: [06:34:55] Testing matching E/Z against Cis/Trans stereo bonds
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
98: .[06:34:55] == testRandomSample
90: [06:34:55]
90:
90: ****
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
90: Pre-condition Violation
90: matches must not be empty
90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp
90: Failed Expression: !matches.empty()
90: ----------
90: Stacktrace:
90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >, std::allocator<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >, std::allocator<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
90: 4# 0x000055FEB489842D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch
90: 5# 0x000055FEB4888C91 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch
90: 6# 0x00007FDA91033CA8 in /lib/x86_64-linux-gnu/libc.so.6
90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
90: 8# 0x000055FEB4888DD1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch
90: ----------
90: ****
90:
90: [06:34:55]
90:
90: ****
90: Pre-condition Violation
90: matches must not be empty
90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp
90: Failed Expression: !matches.empty()
90: ----------
90: Stacktrace:
90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >, std::allocator<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >, std::allocator<std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
90: 4# 0x000055FEB4883420 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch
90: 5# 0x000055FEB4888C91 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch
90: 6# 0x00007FDA91033CA8 in /lib/x86_64-linux-gnu/libc.so.6
90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
90: 8# 0x000055FEB4888DD1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch
90: ----------
90: ****
90:
90: [06:34:55] -------------------------------------
90: [06:34:55] Test substructure matching with a pathological case for symmetric SSSR
98: .[06:34:55] == testRandomSampleAllBBs
90: [06:34:55] -------------------------------------
90: [06:34:55] Test isAtomTerminalRGroupOrQueryHydrogen
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: ........[06:34:55] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q
97: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q'
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: [06:34:55] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q
97: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q'
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: .[06:34:55] reactant atom-mapping number 1 found multiple times.
97: [06:34:55] product atom-mapping number 2 not found in reactants.
97: [06:34:55] mapped atoms in the reactants were not mapped in the products.
97: unmapped numbers are: 4
97: [06:34:55] product atom-mapping number 5 not found in reactants.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
116: [06:34:55] done
86/235 Test #90: testSubstructMatch ..................... Passed 0.46 sec
test 128
Start 128: testFingerprints
128: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints
128: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints
128: Test timeout computed to be: 1500
98: .[06:34:55] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead
98: [06:34:55] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead
98: .[06:34:55] == testRemoveBadMatches
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
116: [06:34:55] -------------------------------------
116: [06:34:55] PBF edge cases.
116: [06:34:55] done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
98: .[06:34:55] == testTimings
87/235 Test #116: testPBF ................................ Passed 0.29 sec
125: Randomness seeded to: 1577171308
125: Warning: Atom Count for residue GLU5A does not match expected count
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
test 129
Start 129: testMHFPFingerprint
129: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint
129: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints
129: Test timeout computed to be: 1500
125: Warning: Atom Count for residue ASN39A does not match expected count
125: Warning: Atom Count for residue GLU53A does not match expected count
125: Warning: Atom Count for residue ARG64A does not match expected count
125: Warning: Atom Count for residue LYS80A does not match expected count
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
111: processing
111: launch :0
111: launch :1
111: launch :2
111: launch :3
88/235 Test #107: filterCatalogTest ...................... Passed 0.39 sec
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
test 130
Start 130: testFingerprintGenerators
130: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators
130: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints
130: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99: .[06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
68: ..............[06:34:55] SMILES Parse Error: syntax error while parsing: invalidsmiles
68: [06:34:55] SMILES Parse Error: check for mistakes around position 1:
68: [06:34:55] invalidsmiles
125: Warning: Atom Count for residue GLU150A does not match expected count
68: [06:34:55] ^
68: [06:34:55] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles'
125: Warning: Atom Count for residue ASN157A does not match expected count
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
129: [06:34:55] -------------------------------------
129: [06:34:55] Test MHFP fingerprint encoder initialization
99: .[06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99: ()
99: ********************************************
99: $RXN
99:
99: RDKit
99:
99: 2 1
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 1 0 0 0 0 0 0999 V2000
99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 1 2 1 0
99: M RGP 1 2 1
99: V 1 halogen.bromine.aromatic
99: V 2 [*:1]
99: M STY 1 1 DAT
99: M SAL 1 1 1
99: M SED 1 [#35&$([Br&$(Br-&!@c)])]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 4 3 0 1 0 0 0 0 0 0999 V2000
99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 2 3 1 0
99: 1 2 1 0
99: 2 4 1 0
99: M RGP 1 1 2
99: V 1 [*:2]
99: V 2 boronicacid
99: M STY 1 1 DAT
99: M SAL 1 1 2
99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 0 0 0 0 0 0 0999 V2000
99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
99: 1 2 1 0
99: M RGP 2 1 1 2 2
99: V 1 [*:1]
99: V 2 [*:2]
99: M END
99:
99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
99: $RXN
99:
99: RDKit
99:
99: 2 1
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 1 0 0 0 0 0 0999 V2000
99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 1 2 1 0
99: M RGP 1 2 1
99: V 1 halogen.bromine.aromatic
99: V 2 [*:1]
99: M STY 1 1 DAT
99: M SAL 1 1 1
99: M SED 1 [#35&$([Br&$(Br-&!@c)])]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 4 3 0 1 0 0 0 0 0 0999 V2000
99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 2 3 1 0
99: 1 2 1 0
99: 2 4 1 0
99: M RGP 1 1 2
99: V 1 [*:2]
99: V 2 boronicacid
99: M STY 1 1 DAT
99: M SAL 1 1 2
99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 0 0 0 0 0 0 0999 V2000
99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
99: 1 2 1 0
99: M RGP 2 1 1 2 2
99: V 1 [*:1]
99: V 2 [*:2]
99: M END
99:
99: ********************************************
99: $RXN
99:
99: RDKit
99:
99: 2 1
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 1 0 0 0 0 0 0999 V2000
99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
99: 1 2 1 0
99: M RGP 1 2 1
99: V 1 halogen.bromine.aromatic
99: V 2 *
99: M STY 1 1 DAT
99: M SAL 1 1 1
99: M SED 1 [#35&$([Br&$(Br-&!@c)])]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 4 3 0 1 0 0 0 0 0 0999 V2000
99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 2 3 1 0
99: 1 2 1 0
99: 2 4 1 0
99: M RGP 1 1 2
99: V 1 *
99: V 2 boronicacid
99: M STY 1 1 DAT
99: M SAL 1 1 2
99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 0 0 0 0 0 0 0999 V2000
99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
99: 1 2 1 0
99: M RGP 2 1 1 2 2
99: V 1 *
99: V 2 *
99: M END
99:
99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
99: $RXN
99:
99: RDKit
99:
99: 2 1
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 1 0 0 0 0 0 0999 V2000
99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 1 2 1 0
99: M RGP 1 2 1
99: V 1 halogen.bromine.aromatic
99: V 2 [*:1]
99: M STY 1 1 DAT
99: M SAL 1 1 1
99: M SED 1 [#35&$([Br&$(Br-&!@c)])]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 4 3 0 1 0 0 0 0 0 0999 V2000
99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 2 3 1 0
99: 1 2 1 0
99: 2 4 1 0
99: M RGP 1 1 2
99: V 1 [*:2]
99: V 2 boronicacid
99: M STY 1 1 DAT
99: M SAL 1 1 2
99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 0 0 0 0 0 0 0999 V2000
99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
99: 1 2 1 0
99: M RGP 2 1 1 2 2
99: V 1 [*:1]
99: V 2 [*:2]
99: M END
99:
99: ********************************************
99: $RXN
99:
99: RDKit
99:
99: 2 1
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 1 0 0 0 0 0 0999 V2000
99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
99: 1 2 1 0
99: M ISO 1 2 1
99: V 1 halogen.bromine.aromatic
99: M STY 1 1 DAT
99: M SAL 1 1 1
99: M SED 1 [#35&$([Br&$(Br-&!@c)])]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 4 3 0 1 0 0 0 0 0 0999 V2000
99: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 2 3 1 0
99: 1 2 1 0
99: 2 4 1 0
99: M ISO 1 1 2
99: V 2 boronicacid
99: M STY 1 1 DAT
99: M SAL 1 1 2
99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 0 0 0 0 0 0 0999 V2000
99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
99: 1 2 1 0
99: M ISO 2 1 1 2 2
99: M END
99:
99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
99: $RXN
99:
99: RDKit
99:
99: 2 1
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 1 0 0 0 0 0 0999 V2000
99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 1 2 1 0
99: M RGP 1 2 1
99: V 1 halogen.bromine.aromatic
99: V 2 [*:1]
99: M STY 1 1 DAT
99: M SAL 1 1 1
99: M SED 1 [#35&$([Br&$(Br-&!@c)])]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 4 3 0 1 0 0 0 0 0 0999 V2000
99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 2 3 1 0
99: 1 2 1 0
99: 2 4 1 0
99: M RGP 1 1 2
99: V 1 [*:2]
99: V 2 boronicacid
99: M STY 1 1 DAT
99: M SAL 1 1 2
99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 0 0 0 0 0 0 0999 V2000
99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
99: 1 2 1 0
99: M RGP 2 1 1 2 2
99: V 1 [*:1]
99: V 2 [*:2]
99: M END
99:
99: ********************************************
99: $RXN
99:
99: RDKit
99:
99: 2 1
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 1 0 0 0 0 0 0999 V2000
99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
99: 1 2 1 0
99: M ISO 1 2 1
99: V 1 halogen.bromine.aromatic
99: M STY 1 1 DAT
99: M SAL 1 1 1
99: M SED 1 [#35&$([Br&$(Br-&!@c)])]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 4 3 0 1 0 0 0 0 0 0999 V2000
99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 2 3 1 0
99: 1 2 1 0
99: 2 4 1 0
99: M ISO 1 1 3
99: V 2 boronicacid
99: M STY 1 1 DAT
99: M SAL 1 1 2
99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 0 0 0 0 0 0 0999 V2000
99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
99: 1 2 1 0
99: M ISO 2 1 1 2 2
99: M END
99: [06:34:55] reactant 0 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] product 0 has no mapped atoms.
99: [06:34:55] Could not find RLabel mapping for atom: 0 in template: 1
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
99: [06:34:55] reactant 1 has no mapped atoms.
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128: Atoms:
128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: 1 conj?: 1
128: 1 1->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: a conj?: 1 aromatic?: 1
128: 6 6->7 order: a conj?: 1 aromatic?: 1
128: 7 7->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: 1 conj?: 1
128: 9 8->10 order: a conj?: 1 aromatic?: 1
128: 10 10->1 order: a conj?: 1 aromatic?: 1
128: 11 7->3 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99: ..
99: ----------------------------------------------------------------------
99: Ran 4 tests in 0.031s
99:
99: OK
128: SMI: Oc1cc2[nH]cnc2c(O)n1
128: Atoms:
128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
99:
99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
99: $RXN
99:
99: RDKit
99:
99: 2 1
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 1 0 0 0 0 0 0999 V2000
99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 1 2 1 0
99: M RGP 1 2 1
99: V 1 halogen.bromine.aromatic
99: V 2 [*:1]
99: M STY 1 1 DAT
99: M SAL 1 1 1
99: M SED 1 [#35&$([Br&$(Br-&!@c)])]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 4 3 0 1 0 0 0 0 0 0999 V2000
99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
99: 2 3 1 0
99: 1 2 1 0
99: 2 4 1 0
99: M ISO 1 1 3
99: V 2 boronicacid
99: M STY 1 1 DAT
99: M SAL 1 1 2
99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)]
99: M END
99: $MOL
99:
99: RDKit 2D
99:
99: 2 1 0 0 0 0 0 0 0 0999 V2000
99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
99: 1 2 1 0
99: M ISO 1 2 2
99: M RGP 1 1 1
99: V 1 [*:1]
99: M END
99:
99: $RXN Failed
128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: 1 conj?: 1
128: 1 1->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: a conj?: 1 aromatic?: 1
128: 6 6->7 order: a conj?: 1 aromatic?: 1
128: 7 7->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: 1 conj?: 1
128: 9 8->10 order: a conj?: 1 aromatic?: 1
128: 10 10->1 order: a conj?: 1 aromatic?: 1
128: 11 7->3 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: SMI: c1(O)cc2[nH]cnc2c(O)n1
128: Atoms:
128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: 1 conj?: 1
128: 1 0->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: a conj?: 1 aromatic?: 1
128: 6 6->7 order: a conj?: 1 aromatic?: 1
128: 7 7->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: 1 conj?: 1
128: 9 8->10 order: a conj?: 1 aromatic?: 1
128: 10 10->0 order: a conj?: 1 aromatic?: 1
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: 11 7->3 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
128: SMI: c1c(O)nc(O)c2c1[nH]cn2
128: Atoms:
128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: a conj?: 1 aromatic?: 1
128: 1 1->2 order: 1 conj?: 1
128: 2 1->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: 1 conj?: 1
128: 5 4->6 order: a conj?: 1 aromatic?: 1
128: 6 6->7 order: a conj?: 1 aromatic?: 1
128: 7 7->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: a conj?: 1 aromatic?: 1
128: 9 9->10 order: a conj?: 1 aromatic?: 1
128: 10 7->0 order: a conj?: 1 aromatic?: 1
128: 11 10->6 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
128: SMI: c12cc(O)nc(O)c1nc[nH]2
128: Atoms:
128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: a conj?: 1 aromatic?: 1
128: 1 1->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: 1 conj?: 1
128: 3 2->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: 1 conj?: 1
128: 6 5->7 order: a conj?: 1 aromatic?: 1
128: 7 7->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: a conj?: 1 aromatic?: 1
128: 9 9->10 order: a conj?: 1 aromatic?: 1
128: 10 7->0 order: a conj?: 1 aromatic?: 1
128: 11 10->0 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: SMI: [nH]1c2cc(O)nc(O)c2nc1
128: Atoms:
128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: a conj?: 1 aromatic?: 1
128: 1 1->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: 1 conj?: 1
128: 4 3->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: a conj?: 1 aromatic?: 1
128: 6 6->7 order: 1 conj?: 1
128: 7 6->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: a conj?: 1 aromatic?: 1
128: 9 9->10 order: a conj?: 1 aromatic?: 1
128: 10 10->0 order: a conj?: 1 aromatic?: 1
128: 11 8->1 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: SMI: c1[nH]c2cc(O)nc(O)c2n1
128: Atoms:
128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
93: [06:34:55] reactant 0 has no mapped atoms.
93: [06:34:55] product 0 has no mapped atoms.
128: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: a conj?: 1 aromatic?: 1
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: 1 1->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: 1 conj?: 1
128: 5 4->6 order: a conj?: 1 aromatic?: 1
128: 6 6->7 order: a conj?: 1 aromatic?: 1
128: 7 7->8 order: 1 conj?: 1
128: 8 7->9 order: a conj?: 1 aromatic?: 1
128: 9 9->10 order: a conj?: 1 aromatic?: 1
128: 10 10->0 order: a conj?: 1 aromatic?: 1
128: 11 9->2 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
93: [06:34:55] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product.
128:
130: [06:34:55] -------------------------------------
130: [06:34:55] Test atom-pair fp generator
128: SMI: n1c[nH]c2cc(O)nc(O)c21
128: Atoms:
128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: a conj?: 1 aromatic?: 1
128: 1 1->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: 1 conj?: 1
128: 6 5->7 order: a conj?: 1 aromatic?: 1
128: 7 7->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: 1 conj?: 1
128: 9 8->10 order: a conj?: 1 aromatic?: 1
128: 10 10->0 order: a conj?: 1 aromatic?: 1
97: ........./build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'>
97: png = open(fname, 'rb').read()
97: ResourceWarning: Enable tracemalloc to get the object allocation traceback
128: 11 10->3 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128:
128: SMI: c12c(cc(O)nc1O)[nH]cn2
128: Atoms:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: a conj?: 1 aromatic?: 1
128: 1 1->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: 1 conj?: 1
128: 4 3->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: a conj?: 1 aromatic?: 1
128: 6 6->7 order: 1 conj?: 1
128: 7 1->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: a conj?: 1 aromatic?: 1
128: 9 9->10 order: a conj?: 1 aromatic?: 1
128: 10 6->0 order: a conj?: 1 aromatic?: 1
128: 11 10->0 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2
128: Atoms:
128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: 1 conj?: 1
128: 1 0->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: 1 conj?: 1
128: 6 5->7 order: a conj?: 1 aromatic?: 1
128: 7 3->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: a conj?: 1 aromatic?: 1
128: 9 9->10 order: a conj?: 1 aromatic?: 1
128: 10 7->0 order: a conj?: 1 aromatic?: 1
128: 11 10->2 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
128: SMI: Oc1c2c(cc(O)n1)[nH]cn2
128: Atoms:
128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: Bonds:
128: 0 0->1 order: 1 conj?: 1
128: 1 1->2 order: a conj?: 1 aromatic?: 1
128: 2 2->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: 1 conj?: 1
128: 6 5->7 order: a conj?: 1 aromatic?: 1
128: 7 3->8 order: a conj?: 1 aromatic?: 1
128: 8 8->9 order: a conj?: 1 aromatic?: 1
128: 9 9->10 order: a conj?: 1 aromatic?: 1
128: 10 7->1 order: a conj?: 1 aromatic?: 1
128: 11 10->2 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
128: SMI: n1c(O)cc2[nH]cnc2c1O
128: Atoms:
128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1
128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1
128: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2
128: Bonds:
128: 0 0->1 order: a conj?: 1 aromatic?: 1
128: 1 1->2 order: 1 conj?: 1
128: 2 1->3 order: a conj?: 1 aromatic?: 1
128: 3 3->4 order: a conj?: 1 aromatic?: 1
128: 4 4->5 order: a conj?: 1 aromatic?: 1
128: 5 5->6 order: a conj?: 1 aromatic?: 1
128: 6 6->7 order: a conj?: 1 aromatic?: 1
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 34
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 36
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 38
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 40
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 42
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 87
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 89
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 91
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 93
97: [06:34:55] Found a SCD/SED line with missing/empty SDT specification at line 95
128: 7 7->8 order: a conj?: 1 aromatic?: 1
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: 8 8->9 order: a conj?: 1 aromatic?: 1
128: 9 9->10 order: 1 conj?: 1
128: 10 9->0 order: a conj?: 1 aromatic?: 1
128: 11 8->4 order: a conj?: 1 aromatic?: 1
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
128:
128:
128:
128:
128:
128:
128:
128:
128: -------------------
128:
129: [06:34:55] done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
129: [06:34:55] -------------------------------------
129: [06:34:55] Test MHFP shingling creation
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test atom-pair fp generator with different arguments
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
89/235 Test #93: testReaction ........................... Passed 0.50 sec
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
test 131
Start 131: fpTestCatch
131: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch
131: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints
131: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: ..[06:34:55] SMARTS Parse Error: syntax error while parsing: boromicacid
97: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid'
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Morgan Fingerprints.
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Morgan Fingerprints using fromAtoms argument.
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Morgan Fingerprints as bit vects.
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Morgan Fingerprints with feature invariants.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: [06:34:55] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide
97: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide'
97: [06:34:55] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride
97: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride'
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test additional Morgan fingerprints options.
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Atom Codes.
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Atom Pairs.
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Atom Pairs part 2.
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Topological Torsions.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Bulk Topological Torsions.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
36: [06:34:55] Maximum BFS search size exceeded.
36: This is likely due to a highly symmetric fused ring system.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
97: [06:34:55] reaction has no reactants
97: [06:34:55] reaction has no products
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
97: [06:34:55] initialization failed
97: [06:34:55] reaction has no reactants
97: [06:34:55] reaction has no products
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97: .[06:34:55] SMARTS Parse Error: syntax error while parsing: boromicacid
97: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid'
97: [06:34:55] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide
97: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide'
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
97: [06:34:55] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride
97: [06:34:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride'
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
97: [06:34:55] reaction has no reactants
97: [06:34:55] reaction has no products
97: [06:34:55] initialization failed
97: [06:34:55] reaction has no reactants
97: [06:34:55] reaction has no products
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
97: .
97: ----------------------------------------------------------------------
97: Ran 54 tests in 0.160s
97:
97: OK
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
97: ********************************************
97: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/AmideBond.rxn
97: <rdkit.Chem.rdChemReactions.ChemicalReaction object at 0x7f6574f13680>
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test atom-pair additional output
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test Folded Atom Pairs.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test Rooted Atom Pairs.
130: [06:34:55] done
130: [06:34:55] -------------------------------------
129: [06:34:55] done
130: [06:34:55] Test ignoring atoms in Atom Pairs.
129: [06:34:55] -------------------------------------
129: [06:34:55] Test MHFP hashing of string and uint arrays
129: [06:34:55] done
129: [06:34:55] -------------------------------------
129: [06:34:55] Test SECFP fingerprint functionality
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test Atom Pairs including info about chirality.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test Morgan Fingerprints.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test morgan fp generator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
112: [06:34:55] done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
112: [06:34:55] -------------------------------------
112: [06:34:55] Test Github #3806: NaNs from AUTOCORR2D descriptor
112: [06:34:55] done
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
90/235 Test #112: testAUTOCORR2D ......................... Passed 0.42 sec
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
test 132
Start 132: fpGenTestCatch
132: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch
132: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints
132: Test timeout computed to be: 1500
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test Morgan Fingerprints using fromAtoms argument.
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test Morgan Fingerprints as bit vects.
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test Morgan Fingerprints with feature invariants.
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test additional Morgan fingerprints options.
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Single atoms setting radius 1 bits in Morgan fingerprints
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test different invariant generator combinations
129: [06:34:55] done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
91/235 Test #129: testMHFPFingerprint .................... Passed 0.08 sec
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test invariant overriding
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test RDKit fp generator
test 133
Start 133: pyTestGenerator
133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/testGenerators.py"
133: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap
133: Test timeout computed to be: 1500
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
30: ...
30: ----------------------------------------------------------------------
30: Ran 12 tests in 0.557s
30:
30: OK
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
131: Randomness seeded to: 1614208654
131: ===============================================================================
131: All tests passed (188 assertions in 16 test cases)
131:
92/235 Test #131: fpTestCatch ............................ Passed 0.04 sec
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
test 134
Start 134: pyTestMHFP
134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/testMHFP.py"
134: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap
134: Test timeout computed to be: 1500
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
120: [06:34:55] done
120: [06:34:55] -------------------------------------
120: [06:34:55] More PMI/NPR tests.
120: [06:34:55] done
120: [06:34:55] -------------------------------------
120: [06:34:55] Basic NPR tests.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
93/235 Test #99: pyChemReactionSanitize ................. Passed 0.52 sec
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
test 135
Start 135: testPartialCharges
135: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges
135: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges
135: Test timeout computed to be: 1500
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
125: Warning: Atom Count for residue GLU5A does not match expected count
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
69: Test
69:
69: marvin03.mrv
69:
69: Test
69:
69: Cubane.mrv
69:
69: Test
69:
69: FalseAtropisomer.mrv
69:
69: Test
69:
69: AtropEnhancedStereo.mrv
69:
69: Test
69:
69: AtropManyChirals.mrv
69:
69: Test
69:
69: AtropManyChiralsEnhanced.mrv
69:
69: Test
69:
69: AtropManyChiralsEnhanced2.mrv
69:
69: Test
69:
69: AtropManyChiralsEnhanced3.mrv
69:
69: Test
69:
69: AtropManyChiralsEnhanced4.mrv
69:
69: Test
69:
69: BMS-986142_3d_chiral.mrv
69:
69: Test
69:
69: BMS-986142_3d.mrv
69:
69: Test
69:
69: BMS-986142_atrop1.mrv
69:
69: Test
69:
69: BMS-986142_atrop2.mrv
69:
69: Test
69:
69: BMS-986142_atrop3.mrv
69:
69: Test
69:
69: BMS-986142_atrop4.mrv
69:
69: Test
69:
69: BMS-986142_atrop5.mrv
69:
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: 300
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
94/235 Test #97: pyChemReactions ........................ Passed 0.56 sec
test 136
Start 136: pyPartialCharges
136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py"
136: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap
136: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
95/235 Test #135: testPartialCharges ..................... Passed 0.03 sec
test 137
Start 137: testMolTransforms
137: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms
137: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms
137: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
92: Randomness seeded to: 700248642
92: ===============================================================================
92: All tests passed (11480 assertions in 38 test cases)
92:
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
96/235 Test #92: testGenericGroups ...................... Passed 0.59 sec
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
test 138
Start 138: molTransformsTestCatch
138: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch
138: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms
138: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
69: Test
69:
69: BMS-986142_atrop6.mrv
69:
69: Test
69:
69: BMS-986142_atrop7.mrv
69:
69: Test
69:
69: BMS-986142_atrop8.mrv
69:
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
68: .....
68: ----------------------------------------------------------------------
68: Ran 19 tests in 0.424s
68:
68: OK
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
69: Test
69:
69: BMS-986142_atropBad2.mrv
69:
69: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
137: ***********************************************************
137: Testing MolTransforms
137: ---------------------------------
137: test1Canonicalization
137:
137: ---------------------------------
137: testGetSetBondLength
137:
137: ---------------------------------
137: testGetSetAngle
137:
137: ---------------------------------
137: testGetSetDihedral
137:
137: ---------------------------------
137: testGetSetDihedralThroughTripleBond
137:
137: ---------------------------------
137: testGithub1262: PMI descriptors incorrect
137:
137: ---------------------------------
137: testGithub1908: CanonicalizeMol() distorting bond lengths
137:
137: ---------------------------------
137: testGithub4302: native computeCanonicalTransform() generates non-canonical coords
137:
137: ---------------------------------
137: testWeightedCentroid
137:
137: ***********************************************************
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
97/235 Test #137: testMolTransforms ...................... Passed 0.06 sec
test 139
Start 139: pyMolTransforms
139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py"
139: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap
139: Test timeout computed to be: 1500
138: Randomness seeded to: 4203172013
138: ===============================================================================
138: All tests passed (4 assertions in 1 test case)
138:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
98/235 Test #138: molTransformsTestCatch ................. Passed 0.06 sec
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
test 140
Start 140: forceFieldHelpersCatch
140: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch
140: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers
140: Test timeout computed to be: 1500
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
69: Test
69:
69: JDQ443_3d.mrv
69:
69: Test
69:
69: JDQ443_atrop1.mrv
69:
69: Test
69:
69: JDQ443_atrop2.mrv
69:
69: Test
69:
69: JDQ443_atrop3.mrv
69:
69: Test
69:
69: JDQ443_atropBad1.mrv
69:
69: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Hashed Atom Pairs.
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Hashed torsions.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Rooted Atom Pairs.
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test ignoring atoms in Atom Pairs.
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Rooted Topological Torsions.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test ignoring atoms in Topological Torsions.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test atom info from morgan fingerprints.
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test atom info from morgan fingerprints including Info Redundant Environments.
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] -------------------------------------
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] -------------------------------------
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
99/235 Test #30: pyForceFieldConstraints ................ Passed 0.93 sec
100/235 Test #68: pyDepictor ............................. Passed 0.76 sec
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
test 141
Start 141: testMMFFForceFieldHelpers
141: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers
141: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF
141: Test timeout computed to be: 1500
test 142
Start 142: testMMFFForceFieldHelpersMultiThread
142: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread
142: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF
142: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
110: .........
110: ----------------------------------------------------------------------
110: Ran 9 tests in 0.085s
110:
110: OK
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
121: =>start test WHIM
128: [06:34:55] -------------------------------------
128: [06:34:55] -------------------------------------
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Atom Pairs including info about chirality.
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test Topological Torsions including info about chirality.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
121: [06:34:55] test on : 365 molecules done
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test GitHub Issue 25: fingerprint backwards compatibility.
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test GitHub Issue 151: PatternFingerprint problems
132: Randomness seeded to: 4175059171
132: ===============================================================================
132: All tests passed (2737 assertions in 7 test cases)
132:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
101/235 Test #121: testWHIM ............................... Passed 0.43 sec
102/235 Test #132: fpGenTestCatch ......................... Passed 0.16 sec
test 143
Start 143: testUFFForceFieldHelpers
143: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers
143: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF
143: Test timeout computed to be: 1500
test 144
Start 144: testCrystalForceField
144: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField
144: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF
144: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Explicit valence for atom # 9 N, 6, is greater than permitted
69: Test
69:
69: RP-6306_atrop1.mrv
69:
69: Test
69:
69: RP-6306_atrop2.mrv
69:
69: Test
69:
69: RP-6306_atrop3.mrv
69:
69: Test
69:
69: RP-6306_atrop4.mrv
69:
69: Test
69:
69: RP-6306_atrop5.mrv
69:
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test 3D atom pairs.
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule
128: [06:34:55] done
128: [06:34:55] -------------------------------------
128: [06:34:55] Test multithreading with the pattern FP
128: reading molecules
69: Test
69:
69: RP-6306_atropBad1.mrv
69:
69: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
141: [06:34:55] -------------------------------------
141: [06:34:55] Test MMFF atom types.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: RP-6306_atropBad2.mrv
69:
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
69: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
142: [06:34:55] -------------------------------------
142: [06:34:55] Test MMFF multithreading
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
141: [06:34:55] done
141: [06:34:55] -------------------------------------
141: [06:34:55] Testing MMFF builder tools.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
140: Randomness seeded to: 3269482022
140: ===============================================================================
140: All tests passed (17 assertions in 2 test cases)
140:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
144: -------------------------------------
144: Test CrystalFF torsional term.
103/235 Test #140: forceFieldHelpersCatch ................. Passed 0.07 sec
115: 400
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
test 145
Start 145: pyForceFieldHelpers
145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py"
145: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap
145: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
114: [06:34:55] -------------------------------------
114: [06:34:55] Test empty molecule BCUT.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
104/235 Test #114: testBCUT ............................... Passed 0.61 sec
test 146
Start 146: testDistGeomHelpers
146: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers
146: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers
146: Test timeout computed to be: 1500
105/235 Test #110: pyFragCatalog .......................... Passed 0.64 sec
test 147
Start 147: distGeomHelpersCatch
147: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch
147: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers
147: Test timeout computed to be: 1500
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
128: pass 1
128: launch :0
128: launch :1
128: launch :2
128: launch :3
141: [06:34:55] done
141: [06:34:55] -------------------------------------
141: [06:34:55] Testing MMFF builder+minimization.
143: [06:34:55] -------------------------------------
143: [06:34:55] Test UFF atom labels.
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
143: [06:34:55] done
143: [06:34:55] -------------------------------------
143: [06:34:55] Test UFF atom typer.
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
143: [06:34:55] done
143: [06:34:55] -------------------------------------
143: [06:34:55] Testing UFF builder tools.
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
143: [06:34:55] done
143: [06:34:55] -------------------------------------
143: [06:34:55] Testing UFF builder+minimization.
126: ..[06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: .[06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:34:55] DEPRECATION WARNING: please use AtomPairGenerator
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
126: ..[06:34:55]
126:
126: ****
126: Pre-condition Violation
126: Number of atom props not equal to number of atoms
126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp
126: Failed Expression: atom_props.size() == num_atoms
126: ----------
126: Stacktrace:
126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector<double, std::allocator<double> > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1
126: 3# 0x00007FF451DD842A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so
126: 4# 0x00007FF451DE8726 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so
126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
126: 6# 0x00007FF455DDD62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
126: 7# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
126: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
126: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
126: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
126: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
126: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
126: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
126: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
126: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
126: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
126: 17# 0x00007FF4539B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
126: 18# 0x00007FF4539B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
126: 19# 0x00007FF4539B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
126: 20# 0x00007FF4539B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
126: 21# 0x00007FF4539B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
126: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
126: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
126: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
126: 25# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
126: 26# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
126: 27# 0x00007FF455DDA3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
126: 28# _PyObject_MakeTpCall in /usr/bin/python3
126: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
126: 30# 0x00000000005BEE79 in /usr/bin/python3
126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
126: 32# 0x0000000000547080 in /usr/bin/python3
126: 33# 0x00000000006AB720 in /usr/bin/python3
126: 34# _PyObject_MakeTpCall in /usr/bin/python3
126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
126: 36# 0x00000000005BEE79 in /usr/bin/python3
126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
126: 38# 0x0000000000547080 in /usr/bin/python3
126: 39# 0x00000000006AB720 in /usr/bin/python3
126: 40# _PyObject_MakeTpCall in /usr/bin/python3
126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
126: 42# 0x00000000005BEE79 in /usr/bin/python3
126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3
126: 44# 0x0000000000547080 in /usr/bin/python3
126: 45# 0x00000000006AB720 in /usr/bin/python3
126: 46# _PyObject_MakeTpCall in /usr/bin/python3
126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3
126: 48# 0x000000000059582E in /usr/bin/python3
126: 49# _PyObject_MakeTpCall in /usr/bin/python3
126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3
126: 51# PyEval_EvalCode in /usr/bin/python3
126: 52# 0x000000000066A861 in /usr/bin/python3
126: 53# 0x000000000066670C in /usr/bin/python3
126: 54# 0x000000000067F713 in /usr/bin/python3
126: 55# 0x000000000067ECE3 in /usr/bin/python3
126: 56# 0x000000000067EB1E in /usr/bin/python3
126: 57# Py_RunMain in /usr/bin/python3
126: 58# Py_BytesMain in /usr/bin/python3
126: 59# 0x00007FF4566A8CA8 in /lib/x86_64-linux-gnu/libc.so.6
126: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
126: 61# _start in /usr/bin/python3
126: ----------
126: ****
126:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: RP-6306_3d.mrv
69:
69: Test
69:
69: Sotorasib_atrop1.mrv
69:
69: Test
69:
69: Sotorasib_atrop2.mrv
69:
69: Test
69:
69: Sotorasib_atrop3.mrv
69:
69: Test
69:
69: Sotorasib_atrop4.mrv
69:
69: Test
69:
69: Sotorasib_atrop5.mrv
69:
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
69: [06:34:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: Test
69:
69: Sotorasib_atropBad1.mrv
69:
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
69: [06:34:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
146: [06:34:55] ********************************************************
146: [06:34:55] Testing DistGeomHelpers
146: [06:34:55] ---------------------------------
146: [06:34:55] test2
146:
146: go
146: -------------------------------------
146:
69: Test
69:
69: Sotorasib_atropBad2.mrv
69:
126: ...Warning: Atom Count for residue GLU5A does not match expected count
120: [06:34:55] done
120: [06:34:55] -------------------------------------
120: [06:34:55] PMI edge cases.
69: [06:34:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20
120: [06:34:55] done
120: [06:34:55] -------------------------------------
120: [06:34:55] NPR edge cases.
120: [06:34:55] done
120: [06:34:55] -------------------------------------
120: [06:34:55] 3D descriptors.
120: [06:34:55] done
120: [06:34:55] -------------------------------------
120: [06:34:55] 3D descriptor edge cases.
120: [06:34:55] done
120: [06:34:55] -------------------------------------
120: [06:34:55] Inertial shape factor.
120: [06:34:55] done
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
126: Warning: Atom Count for residue ASN39A does not match expected count
126: Warning: Atom Count for residue GLU53A does not match expected count
106/235 Test #120: test3D ................................. Passed 0.58 sec
test 148
Start 148: pyDistGeomHelpers
148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py"
148: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap
148: Test timeout computed to be: 1500
126: Warning: Atom Count for residue ARG64A does not match expected count
126: Warning: Atom Count for residue LYS80A does not match expected count
147: Randomness seeded to: 816238431
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
117: =>start test rdf custom
126: Warning: Atom Count for residue GLU150A does not match expected count
117: [06:34:55] test on : 365 molecules done
126: Warning: Atom Count for residue ASN157A does not match expected count
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
89: [06:34:55] Explicit valence for atom # 3 Al, 6, is greater than permitted
123: =>start test autocorr3D
123: [06:34:55] test on : 365 molecules done
107/235 Test #123: testAUTOCORR3D ......................... Passed 0.53 sec
142: processing
142: launch :0
142: launch :1
142: launch :2
142: launch :3
142: launch :4
142: launch :5
142: launch :6
142: launch :7
142: launch :8
142: launch :9
142: launch :10
142: launch :11
142: launch :12
142: launch :13
142: launch :14
142: launch :15
142: launch :16
142: launch :17
142: launch :18
142: launch :19
142: launch :20
142: launch :21
142: launch :22
142: launch :23
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: [06:34:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
115: Elapsed time: 0.73302 s
115: Errors:0
115: [06:34:55] test on : 500 molecules done
141: [06:34:55] done
141: [06:34:55] -------------------------------------
141: [06:34:55] Testing Issue239.
141: [06:34:56] done
141: [06:34:56] -------------------------------------
141: [06:34:56] Testing calcEnergy with passed coords.
134: ..
134: ----------------------------------------------------------------------
134: Ran 2 tests in 0.038s
134:
134: OK
125: Warning: Atom Count for residue ASN39A does not match expected count
147: [06:34:55] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)]
147: [06:34:55] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:55] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)]
147: [06:34:55] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)]
147: [06:34:55] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:55] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)]
147: [06:34:55] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)]
147: [06:34:56] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:56] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:56] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [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)]
147: -----------
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:56] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:56] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)]
147: [06:34:56] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)]
147: -----------
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)]
147: [06:34:56] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)]
147: -----------
147: -----------
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)]
147: [06:34:56] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)]
147: [06:34:56] [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)]
126: Warning: Atom Count for residue GLU5A does not match expected count
127: ........
127: ----------------------------------------------------------------------
127: Ran 8 tests in 0.193s
127:
127: OK
89: [06:34:55] Explicit valence for atom # 4 Al, 6, is greater than permitted
89: [06:34:56] Explicit valence for atom # 10 Si, 6, is greater than permitted
130: [06:34:55] done
130: [06:34:55] -------------------------------------
130: [06:34:55] Test unfolded version of RDKFP
130: [06:34:55] -------------------------------------
130: [06:34:55] Test topological torsion fp generator
130: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test Topological Torsions.
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test Folded torsions.
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test Bulk Topological Torsions.
118: =>start test rdf
118: [06:34:56] test on : 365 molecules done
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Testing UFF special cases.
143: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 0
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Testing Issue239.
test 149
Start 149: testMolAlign
149: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign
149: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign
149: Test timeout computed to be: 1500
69: Test
69:
69: Sotorasib_3d.mrv
69:
69: Test
69:
69: ZM374979_atrop1.mrv
69:
69: Test
69:
69: ZM374979_atrop2.mrv
69:
69: Test
69:
69: ZM374979_atrop3.mrv
69:
69: Test
69:
69: ZM374979_atropBad1.mrv
69:
69: [06:34:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
69: Test
69:
69: mrtx1719_3d.mrv
69:
69: Test
69:
69: mrtx1719_atrop1.mrv
69:
69: Test
69:
69: mrtx1719_atrop2.mrv
69:
69: Test
69:
69: mrtx1719_atrop3.mrv
69:
69: Test
69:
69: mrtx1719_atropBad1.mrv
69:
69: [06:34:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16
128: pass 2
128: launch :0
128: launch :1
128: launch :2
128: launch :3
139: ........
139: ----------------------------------------------------------------------
139: Ran 8 tests in 0.034s
139:
139: OK
109: [06:34:56]
109:
109: ****
109: Invariant Violation
109: nonsense
109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp
109: Failed Expression: token != tokens.end()
109: ----------
109: Stacktrace:
109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
109: 2# 0x00007FAC3E201DFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1
109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1
109: 4# 0x000055A89C9B7183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: 5# 0x000055A89C9B4731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: 6# 0x00007FAC3D433CA8 in /lib/x86_64-linux-gnu/libc.so.6
109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
109: 8# 0x000055A89C9B4861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: ----------
109: ****
109:
109: [06:34:56]
109:
109: ****
109: Invariant Violation
109: nonsense no new line
109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp
109: Failed Expression: token != tokens.end()
109: ----------
109: Stacktrace:
109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
109: 2# 0x00007FAC3E201DFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1
109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1
109: 4# 0x000055A89C9B7183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: 5# 0x000055A89C9B4731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: 6# 0x00007FAC3D433CA8 in /lib/x86_64-linux-gnu/libc.so.6
109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
109: 8# 0x000055A89C9B4861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: ----------
109: ****
109:
109: [06:34:56]
109:
109: ****
109: Invariant Violation
109: nonsense with tab
109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp
109: Failed Expression: token != tokens.end()
109: ----------
109: Stacktrace:
109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
109: 2# 0x00007FAC3E201DFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1
109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1
109: 4# 0x000055A89C9B7183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: 5# 0x000055A89C9B4731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: 6# 0x00007FAC3D433CA8 in /lib/x86_64-linux-gnu/libc.so.6
109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
109: 8# 0x000055A89C9B4861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog
109: ----------
109: ****
109:
70: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored
70: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored
70: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored
70: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored
70: [06:34:56] deprecated group abbreviation ignored on line 24
70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*]
70: [06:34:56]
70:
70: ****
70: Post-condition Violation
70: Element 'Mv' not found
70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h
70: Failed Expression: anum > -1
70: ----------
70: Stacktrace:
70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 3# 0x00007F82450C8511 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 4# 0x00007F82450D1DEA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 5# 0x00007F82450D216D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 9# 0x0000563A13E9DCB5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 10# 0x0000563A13F04492 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 11# 0x0000563A13E849B3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 12# 0x00007F8244633CA8 in /lib/x86_64-linux-gnu/libc.so.6
70: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
70: 14# 0x0000563A13E84B61 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: ----------
70: ****
70:
108/235 Test #109: testFragCatalog ........................ Passed 0.89 sec
109/235 Test #115: testEEM ................................ Passed 0.85 sec
110/235 Test #118: testRDF ................................ Passed 0.80 sec
111/235 Test #127: pyMolDescriptors3D ..................... Passed 0.59 sec
112/235 Test #134: pyTestMHFP ............................. Passed 0.44 sec
113/235 Test #144: testCrystalForceField .................. Passed 0.28 sec
141: [06:34:56] done
141: [06:34:56] -------------------------------------
141: [06:34:56] Testing calcGrad.
test 150
Start 150: testO3AAlign
150: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign
150: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign
150: Test timeout computed to be: 1500
test 151
Start 151: molAlignCatchTest
151: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest
151: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign
151: Test timeout computed to be: 1500
test 152
Start 152: pyMolAlign
152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap/testMolAlign.py"
152: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap
152: Test timeout computed to be: 1500
test 153
Start 153: testFeatures
153: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures
153: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures
153: Test timeout computed to be: 1500
test 154
Start 154: pyChemicalFeatures
154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py"
154: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap
154: Test timeout computed to be: 1500
test 155
Start 155: testShapeHelpers
155: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers
155: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers
155: Test timeout computed to be: 1500
141: [06:34:56] done
141: [06:34:56] -------------------------------------
141: [06:34:56] Testing Issue242.
125: Warning: Atom Count for residue GLU53A does not match expected count
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Testing calcEnergy with passed coords.
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Testing calcGrad.
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Testing SFIssue1653802.
147: [06:34:56] UFFTYPER: Unrecognized atom type: Pt5+2 (1)
119: =>start test MORSE
119: =>read file
119: [06:34:56] test on : 365 molecules done
114/235 Test #119: testMORSE .............................. Passed 0.82 sec
115/235 Test #139: pyMolTransforms ........................ Passed 0.37 sec
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Testing SFIssue2378119.
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 1
test 156
Start 156: pyShapeHelpers
156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py"
156: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap
156: Test timeout computed to be: 1500
test 157
Start 157: testMolCatalog
157: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog
157: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog
157: Test timeout computed to be: 1500
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Test UFF force-field parameter getters.
143: [06:34:56] -------------------------------------
143: [06:34:56] Testing handling missing parameters.
143: [06:34:56] UFFTYPER: Unrecognized hybridization for atom: 0
143: [06:34:56] UFFTYPER: Unrecognized atom type: Cu+1 (0)
143: [06:34:56] UFFTYPER: Unrecognized hybridization for atom: 0
143: [06:34:56] UFFTYPER: Unrecognized atom type: Cu+1 (0)
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Testing SFIssue3009337.
143: [06:34:56] done
143: [06:34:56] -------------------------------------
143: [06:34:56] Test UFF multithreading
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 1
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 1
133: ..............
133: ----------------------------------------------------------------------
133: Ran 14 tests in 0.149s
133:
133: OK
141: [06:34:56] done
141: [06:34:56] -------------------------------------
141: [06:34:56] Testing github 308: crash during MMFF parameterization .
141: [06:34:56] -------------------------------------
141: [06:34:56] Testing SFIssue1653802.
141: [06:34:56] done
141: [06:34:56] -------------------------------------
141: [06:34:56] Testing SFIssue2378119.
141: [06:34:56] done
141: [06:34:56] -------------------------------------
141: [06:34:56] Test MMFF force-field parameter getters.
141: [06:34:56] -------------------------------------
141: [06:34:56] Test MMFF multithreading
153: [06:34:56] -------------------------------------
153: [06:34:56] AtomType parser testing.
153: [06:34:56] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]
153: [06:34:56] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]'
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] FeatureDefinition parser testing.
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] Test pulling feat defs from a string.
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] FeatureDef functionality testing.
69: Test
69:
69: FalseAtropisomer.mrv
69:
69: Test
69:
69: AtropEnhancedStereo.mrv
69:
69: Test
69:
69: AtropManyChirals.mrv
69:
69: Test
69:
69: AtropManyChiralsEnhanced.mrv
69:
69: Test
69:
69: AtropManyChiralsEnhanced2.mrv
69:
69: Test
69:
69: AtropManyChiralsEnhanced3.mrv
69:
69: Test
69:
69: AtropManyChiralsEnhanced4.mrv
69:
69: Test
69:
69: BMS-986142_3d_chiral.mrv
69:
69: Test
69:
69: BMS-986142_3d.mrv
69:
69: Test
69:
69: BMS-986142_atrop1.mrv
69:
69: Test
69:
69: BMS-986142_atrop2.mrv
69:
69: Test
69:
69: BMS-986142_atrop3.mrv
69:
69: Test
69:
69: BMS-986142_atrop4.mrv
69:
69: Test
69:
69: BMS-986142_atrop5.mrv
69:
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: ..[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
141: generating reference data
69: Test
69:
69: BMS-986142_atrop6.mrv
69:
69: Test
69:
69: BMS-986142_atrop7.mrv
69:
69: Test
69:
69: BMS-986142_atrop8.mrv
69:
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
143: generating reference data
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] FeatureFactory testing.
153: [06:34:56] 1
153: [06:34:56] 2
153: [06:34:56] 3
153: [06:34:56] 4
153: [06:34:56] 5
153: [06:34:56] 6
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] Feature Location testing.
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] Test building a FeatureFactory from a file
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] Testing Issue 224.
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] Testing Issue 225.
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] Test Issue346
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] Test Issue347
153: [06:34:56] done
153: [06:34:56] -------------------------------------
153: [06:34:56] Testing Issue 348.
153: [06:34:56] SMARTS Parse Error: syntax error while parsing: [C[C]
153: [06:34:56] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]'
153: [06:34:56] -------------------------------------
153: [06:34:56] Testing Nested AtomType definitions.
153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])]
153: [06:34:56] -------------------------------------
153: [06:34:56] Testing Github Issue #252: crash when calling getPos() with no conformer.
153: [06:34:56] expect a precondition failure message below
153: [06:34:56]
153:
153: ****
153: Pre-condition Violation
153: molecule has no conformers
153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp
153: Failed Expression: dp_mol->getNumConformers()
153: ----------
153: Stacktrace:
153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1
153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1
153: 4# 0x000055B887242E50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures
153: 5# 0x000055B887237743 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures
153: 6# 0x00007FDE1EA33CA8 in /lib/x86_64-linux-gnu/libc.so.6
153: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
153: 8# 0x000055B887237841 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures
153: ----------
153: ****
153:
153: [06:34:56] Done
153: [06:34:56] -------------------------------------
153: [06:34:56] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol()
153: [06:34:56] done
69: Test
69:
69: BMS-986142_atropBad2.mrv
69:
69: [06:34:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29
116/235 Test #153: testFeatures ........................... Passed 0.06 sec
test 158
Start 158: pyMolCatalog
158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap/rough_test.py"
158: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap
158: Test timeout computed to be: 1500
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
142: done
125: Warning: Atom Count for residue ARG64A does not match expected count
117/235 Test #157: testMolCatalog ......................... Passed 0.05 sec
test 159
Start 159: moldraw2DTest1
159: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1
159: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D
159: Test timeout computed to be: 1500
36: [06:34:56] Maximum BFS search size exceeded.
36: This is likely due to a highly symmetric fused ring system.
69: Test
69:
69: JDQ443_3d.mrv
69:
69: Test
69:
69: JDQ443_atrop1.mrv
69:
69: Test
69:
69: JDQ443_atrop2.mrv
69:
69: Test
69:
69: JDQ443_atrop3.mrv
69:
69: Test
69:
69: JDQ443_atropBad1.mrv
69:
69: [06:34:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21
142: [06:34:56] done
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test Rooted Topological Torsions.
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test ignoring atoms in Topological Torsions.
130: [06:34:56] done
130: [06:34:56] -------------------------------------
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
130: [06:34:56] -------------------------------------
130: [06:34:56] Test Topological Torsions including info about chirality.
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test GitHub Issue 25: fingerprint backwards compatibility.
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP.
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test convenience and bulk fp calculation functions
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
155: ***********************************************************
155: Testing ShapeHelpers
155: ---------------------------------
155: test1Encode
155:
155: ---------------------------------
155: test2Compare
155:
155: ---------------------------------
155: testGithub4364
155:
155: ***********************************************************
70: [06:34:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
118/235 Test #155: testShapeHelpers ....................... Passed 0.09 sec
test 160
Start 160: moldraw2DTestCatch
160: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D
160: Test timeout computed to be: 1500
70: [06:34:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
119/235 Test #133: pyTestGenerator ........................ Passed 0.57 sec
test 161
Start 161: moldraw2DRxnTest1
161: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1
161: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D
161: Test timeout computed to be: 1500
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 5
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 5
151: Randomness seeded to: 3817447685
151: 57765140
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: .[06:34:56] UFFTYPER: Unrecognized hybridization for atom: 0
145: [06:34:56] UFFTYPER: Unrecognized atom type: Cu+1 (0)
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
69: Test
69:
69: RP-6306_atrop1.mrv
69:
69: Test
69:
69: RP-6306_atrop2.mrv
69:
69: Test
69:
69: RP-6306_atrop3.mrv
69:
69: Test
69:
69: RP-6306_atrop4.mrv
69:
69: Test
69:
69: RP-6306_atrop5.mrv
69:
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: .[06:34:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: .[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: ...[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
69: Test
69:
69: RP-6306_atropBad1.mrv
69:
69: [06:34:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 5
159: ----------------- Test 1
69: Test
69:
69: RP-6306_atropBad2.mrv
69:
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored
69: [06:34:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8
120/235 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.46 sec
108: .............[06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
test 162
Start 162: pyMolDraw2D
162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py"
162: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap
162: Test timeout computed to be: 1500
148: .[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
36: F/C=C/Cl
36: [H]/C(F)=C(/[H])Cl
36: F/C=C/Cl
36: F/C=C/Cl
36: C/C(F)=C(/C)Cl
36: [06:34:56] -----------------------
36: Testing isRingFused
145: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
151: 46784145
89: [06:34:56] Explicit valence for atom # 2 O, 4, is greater than permitted
161: ----------------- Test 1
149: ***********************************************************
149: Testing MolAlign
149: ---------------------------------
149: test1MolAlign
149:
149: ---------------------------------
149: test1GetBestRMS
149:
149: ---------------------------------
149: test1MolWithQueryAlign
149:
149: ---------------------------------
149: test2AtomMap
149:
149: ---------------------------------
149: test3Weights
149:
149: ---------------------------------
149: testIssue241
149:
149: ***********************************************************
121/235 Test #36: graphmolMolOpsTest ..................... Passed 1.43 sec
122/235 Test #149: testMolAlign ........................... Passed 0.22 sec
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
test 163
Start 163: testFMCS
163: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS
163: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS
163: Test timeout computed to be: 1500
test 164
Start 164: pyFMCS
164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap/testFMCS.py"
164: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap
164: Test timeout computed to be: 1500
89: [06:34:56] Explicit valence for atom # 3 Be, 4, is greater than permitted
89: [06:34:56] Explicit valence for atom # 3 Al, 6, is greater than permitted
136: .......
136: ----------------------------------------------------------------------
136: Ran 7 tests in 0.318s
136:
136: OK
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
108: [06:34:56] SMILES Parse Error: syntax error while parsing: ---
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] ---
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES '---' for input: '---'
108: [06:34:56] dasfsadf
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: ..[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
126: Warning: Atom Count for residue ASN39A does not match expected count
160: Randomness seeded to: 529472454
160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U
70: ----------------------------------
70: ----------------------------------
70: [06:34:56]
70:
70: ****
70: Pre-condition Violation
70: rlabel out of range for MDL files
70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp
70: Failed Expression: rlabel >= 0 && rlabel < 100
70: ----------
70: Stacktrace:
70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
70: 3# 0x0000563A13EAB09F in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 4# 0x0000563A13F0450A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 5# 0x0000563A13E849B3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 6# 0x00007F8244633CA8 in /lib/x86_64-linux-gnu/libc.so.6
70: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
70: 8# 0x0000563A13E84B61 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: ----------
70: ****
70:
70: [06:34:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 6
159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U
145: ...
145: ----------------------------------------------------------------------
145: Ran 19 tests in 0.182s
145:
145: OK
159: Done
159: ----------------- Test 2
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 6
69: Test
69:
69: RP-6306_3d.mrv
69:
69: Test
69:
69: Sotorasib_atrop1.mrv
69:
69: Test
69:
69: Sotorasib_atrop2.mrv
69:
69: Test
69:
69: Sotorasib_atrop3.mrv
69:
69: Test
69:
69: Sotorasib_atrop4.mrv
69:
69: Test
69:
69: Sotorasib_atrop5.mrv
69:
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
69: [06:34:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
89: [06:34:56] Explicit valence for atom # 27 P, 6, is greater than permitted
69: Test
69:
69: Sotorasib_atropBad1.mrv
69:
69: [06:34:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20
69: Test
69:
69: Sotorasib_atropBad2.mrv
69:
69: [06:34:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20
159: file test2_1.png gave hash 3164573255U not the expected 638584804U
148: ..[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
147: [06:34:56] UFFTYPER: Unrecognized charge state for atom: 6
161: file rxn_test1_1.png gave hash 196847225U not the expected 801892091U
125: Warning: Atom Count for residue LYS80A does not match expected count
148: .[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
159: file test2_2.png gave hash 3715219030U not the expected 610424244U
61: Test
61:
61: AtropCanon1.cxsmi
61:
61: Test
61:
61: AtropCanon2.cxsmi
61:
61: Test
61:
61: AtropCanon3.cxsmi
61:
61: Test
61:
61: BMS-986142_3d_chiral.cxsmi
61:
61: Test
61:
61: BMS-986142_3d.cxsmi
61:
61: ===============================================================================
61: All tests passed (2445 assertions in 29 test cases)
61:
123/235 Test #61: cxsmilesTest ........................... Passed 1.38 sec
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
test 165
Start 165: FMCStest
165: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest
165: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test
165: Test timeout computed to be: 1500
160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U
69: Test
69:
69: Sotorasib_3d.mrv
69:
69: Test
69:
69: ZM374979_atrop1.mrv
69:
69: Test
69:
69: ZM374979_atrop2.mrv
69:
69: Test
69:
69: ZM374979_atrop3.mrv
69:
69: Test
69:
69: ZM374979_atropBad1.mrv
69:
69: [06:34:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
124/235 Test #145: pyForceFieldHelpers .................... Passed 0.54 sec
test 166
Start 166: molHashCatchTest
166: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest
166: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash
166: Test timeout computed to be: 1500
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
125/235 Test #136: pyPartialCharges ....................... Passed 0.69 sec
test 167
Start 167: pyMolHash
167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap/testMolHash.py"
167: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap
167: Test timeout computed to be: 1500
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
159: Done
159: ----------------- Test 4
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_15113.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_16613.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_30745.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_30861.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_31495.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_34869.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_36158.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_36559.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_37434.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_39147.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_43754.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_44011.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_44158.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_48076.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_48961.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_49648.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_49703.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51128.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51343.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_51842.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_54554.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_100_55749.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_17256.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20244.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20245.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30149.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30499.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_36186.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_39262.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_43966.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_45279.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_48029.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49064.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49801.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_50681.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_54039.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58265.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58358.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58866.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10188_60810.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21358.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21597.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30111.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30349.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31746.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31822.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_35220.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37603.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37964.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_39508.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42164.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42577.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_44072.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_45522.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46700.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46719.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46744.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_48517.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_49087.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_50034.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_51475.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53483.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53506.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_54598.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55614.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55737.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57090.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57705.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57785.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_58463.txt
165:
165: testChEMBfopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: L_Txt() chembl_II_sets/Target_no_10193_58700.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61003.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61349.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_38526.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_50778.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_52179.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10260_54285.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_30224.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_31222.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37349.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37369.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37465.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37541.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_38371.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44314.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44578.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_45765.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_46281.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_47928.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_50624.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51341.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51662.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51767.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53081.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53396.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53407.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_58823.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_59190.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_60672.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10280_61176.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_20905.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30074.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30175.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30423.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_31555.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_34878.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_35926.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10434_42168.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_20859.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30060.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30061.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30606.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_30866.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_31249.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_34921.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_35188.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_36636.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_37466.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_39202.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_43952.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49345.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49591.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_49854.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_51416.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_53537.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_58879.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_60679.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_107_61269.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_20600.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_20859.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30060.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30606.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_30866.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_31558.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_35188.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_37466.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_43875.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_48911.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_49591.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_49854.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: no_108_57887.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_60679.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_108_6857.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_15478.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_20853.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30840.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30862.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30918.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30994.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31014.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31508.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31623.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35003.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35004.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35281.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35957.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36520.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36641.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_38586.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_44431.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_45093.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_51302.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5247.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_52937.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_57198.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5739.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_10980_6535.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20205.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20986.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_30091.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34698.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34705.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37038.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37272.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37447.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38909.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38953.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_39472.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_45825.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_47179.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49028.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49860.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_51984.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53395.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53826.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54121.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54530.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_55738.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_57725.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11140_58590.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_20432.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_30331.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_37956.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_48114.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11365_58566.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34731.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34818.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37318.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37339.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37564.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39504.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39561.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46082.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46089.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47349.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47757.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_51593.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_54754.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58262.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58958.txt
165:
165: testChEMBL_Txt(fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: ) chembl_II_sets/Target_no_114_16827.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_20503.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_20724.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30254.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30321.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_30572.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31116.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31281.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_31443.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_34747.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_34920.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_35040.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_36623.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_37136.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_37208.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_38298.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_38554.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_39088.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_39543.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_44049.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_44562.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_45180.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_45867.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_46087.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_46829.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_47546.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_48395.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_50461.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_50765.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_51669.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_52381.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_57231.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_114_58246.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_30999.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31021.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31650.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_35011.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_37014.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_44598.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_48446.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50614.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50615.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50618.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11534_51950.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_31616.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_38381.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_45757.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_46816.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_50701.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_54049.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_57890.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11575_61045.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_30194.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_31421.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_35538.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_55727.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_60676.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_61130.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_11631_6444.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_15623.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_20096.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_21591.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30184.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30380.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30745.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_30861.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_31619.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_34869.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_35284.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_36158.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_36915.txt
165:
165: testChEMBL_Txfopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: t() chembl_II_sets/Target_no_121_37434.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_37541.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_37677.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_38837.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_39530.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_43793.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44158.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44164.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44579.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44593.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44692.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_44914.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_45878.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48050.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48706.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48944.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_48961.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_49880.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_50055.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_50512.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_51064.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_53537.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_55749.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_58879.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_121_6876.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_44664.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_46451.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_50640.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_56102.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_58015.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59089.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59092.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12209_61340.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_31458.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_38481.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_42104.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49475.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49933.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12252_50558.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_126_37249.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_126_39117.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_126_48227.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_126_48229.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_126_53969.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_126_54262.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_126_55353.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_126_61212.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20250.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20506.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20626.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20689.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_21358.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30158.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30349.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_34843.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_35220.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36318.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36800.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_39349.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45385.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45676.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46700.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46719.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_48517.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_52690.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_53483.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_55435.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_56102.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58015.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58375.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_1295fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: 2_58700.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_16724.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_2710.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_30128.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_31250.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_35519.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_36905.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_46788.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_4737.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_55736.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_13001_57473.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_16146.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30313.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30539.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30653.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_30988.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_31179.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_31339.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_3525.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_36886.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_37020.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_38128.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_43952.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_45210.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_45899.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_47889.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_51800.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_53158.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_5330.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_55648.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_56096.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57287.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57399.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_57606.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_58470.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_130_60894.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_15010.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20304.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20542.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_20788.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_21358.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_30349.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31103.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31764.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_31822.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_35220.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_37964.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_42164.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_44072.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_45522.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_46719.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_46744.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_48416.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_49740.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_50034.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_50640.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53483.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53506.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_53814.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_55435.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_56074.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_56107.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57090.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57705.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57785.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_57861.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_58583.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_59089.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_15_59092.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_20600.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_30764.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_34876.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_37427.tfopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: xt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_38266.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_45283.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_46990.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_47123.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_47900.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48050.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48062.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_48076.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_50718.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_50972.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_51372.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_51830.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_53049.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_53505.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54021.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54565.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_54570.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_57666.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_57890.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58072.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58634.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_58643.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59080.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59202.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_59346.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_60379.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_60385.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_165_61098.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_31154.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_35648.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_48914.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_51975.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_52435.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_55790.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_58958.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_17045_61146.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20191.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20562.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20606.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20607.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30003.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30402.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30726.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30924.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31457.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31460.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31600.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31620.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31640.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31782.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31797.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31829.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31856.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34690.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34691.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34694.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_35712.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37497.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37539.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48070.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48219.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48824.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48902.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_52867.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_53534.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_54570.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_58727.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60159.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60661.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_30037.txt
165:
165: testChEMBL_Txt() chefopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: mbl_II_sets/Target_no_259_34734.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_35365.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_35787.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_36793.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_37845.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_38328.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_39374.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_43936.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44059.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44405.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_44424.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_45166.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_46158.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_46425.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_47187.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48435.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48817.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48849.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48957.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_48965.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_49519.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_49921.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_50392.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_50972.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_52405.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_52442.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_53169.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_54640.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_57207.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_58537.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_58920.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_259_60358.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_25_16077.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_25_34943.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_25_36391.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_25_36574.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_25_52906.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_25_54642.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_16385.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_20333.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_20774.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_35825.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_37637.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_47741.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_48567.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_48841.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_49589.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_50564.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_51201.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_53150.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_55747.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_43_58276.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_20813.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_2331.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_2391.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30374.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30512.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_30796.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_31058.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_31450.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_36609.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_36636.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_38266.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_43800.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_47621.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49433.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49550.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_49865.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_51005.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_52373.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_53878.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt
165:
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U
160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U
160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U
161: file rxn_test1_2.png gave hash 1760761969U not the expected 507435337U
161: file rxn_test1_3.png gave hash 3097655468U not the expected 1590809137U
69: Test
69:
69: mrtx1719_3d.mrv
69:
69: Test
69:
69: mrtx1719_atrop1.mrv
69:
69: Test
69:
69: mrtx1719_atrop2.mrv
69:
69: Test
69:
69: mrtx1719_atrop3.mrv
69:
69: Test
69:
69: mrtx1719_atropBad1.mrv
69:
69: [06:34:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165:
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_57618.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_59484.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_51_6563.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_61_16845.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_61_37106.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_61_37272.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_61_47947.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_61_50754.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_61_55800.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_61_57380.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_65_35328.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_65_36137.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_65_38826.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_65_44596.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_65_51275.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_65_55671.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_20155.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30616.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30653.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_30988.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31339.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31527.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_31631.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36047.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36568.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_36636.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_37020.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_38128.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_43952.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_45210.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_47889.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_51064.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_51800.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_5330.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_57508.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_58470.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_72_60894.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_20730.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_20753.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_30097.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_30663.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35365.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35375.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_35918.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36010.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36780.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_36793.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_37845.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_39110.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_39546.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_43936.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44405.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44424.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_44683.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_45166.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_46648.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_46986.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_47070.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_47187.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_48435.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_48817.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49138.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49460.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49519.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49532.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_49829.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_50608.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_54640.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_87_61082.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_90_15727.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_90_20155.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_90_30407.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_90_3525.txt
165:
165: testChEMBfopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: fopen testChEMBL_Txt(): No such file or directory
165: L_Txt() chembl_II_sets/Target_no_93_12377.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_93_1308.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_93_34759.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_93_35447.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_93_42214.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_93_45877.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_93_47082.txt
165:
165: testChEMBL_Txt() chembl_II_sets/Target_no_93_57082.txt
165:
165: testFileSDF_RandomSet(): benchmark/chembl13-10000-random-pairs.sdf
165: ERROR: RDKit could not load input file
165:
165: testFileSDF_RandomSet(): benchmark/chembl13_pairs.smi
165: ERROR: RDKit could not load input file
165:
165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_2.smi
165: ERROR: RDKit could not load input file
165:
165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_10.smi
165: ERROR: RDKit could not load input file
165:
165: testFileSDF_RandomSet(): benchmark/chembl13_knearest_100.smi
165: ERROR: RDKit could not load input file
165:
165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_80.smi
165: ERROR: RDKit could not load input file
165:
165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi
165: ERROR: RDKit could not load input file
159: file test4_1.png gave hash 3656546255U not the expected 3993974247U
159: Done
159: ----------------- Test 5
159: file test5_1.png gave hash 3659160374U not the expected 571291290U
159: file test5_2.png gave hash 3029052427U not the expected 97265124U
159: file test5_3.png gave hash 979411683U not the expected 606188176U
159: Done
159: ----------------- Test 6 (atom labels)
154: .[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
154: .[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
126: Warning: Atom Count for residue GLU53A does not match expected count
108: .[06:34:56] SMILES Parse Error: syntax error while parsing: mydoghasfleas
108: [06:34:56] SMILES Parse Error: check for mistakes around position 1:
108: [06:34:56] mydoghasfleas
108: [06:34:56] ^
108: [06:34:56] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas'
126/235 Test #165: FMCStest ............................... Passed 0.11 sec
166: Randomness seeded to: 3525773153
166: ===============================================================================
166: All tests passed (363 assertions in 14 test cases)
166:
127/235 Test #166: molHashCatchTest ....................... Passed 0.10 sec
69: Test
69:
69: AlexRxn.mrv
69:
69: Test
69:
69: BadReactionSign.mrv
69:
69: Test
69:
69: bondArray_node.mrv
69:
69: Test
69:
69: marvin03.mrv
69:
69: Test
69:
69: marvin04.mrv
69:
69: Test
69:
69: marvin08.mrv
69:
69: Test
69:
69: marvin09.mrv
69:
69: Test
69:
69: marvin11.mrv
69:
69: Test
69:
69: marvin05.mrv
69:
69: Test
69:
69: EmptyRxn.mrv
69:
69: [06:34:56] initialization failed
test 168
Start 168: testMMPA
168: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA
168: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA
168: Test timeout computed to be: 1500
test 169
Start 169: pyMMPA
169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/testMMPA.py"
169: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap
169: Test timeout computed to be: 1500
160: file testGithub3226_1.png gave hash 3357385997U not the expected 3165135374U
143: processing
143: launch :0
143: launch :1
143: launch :2
143: [06:34:56] Rep: 0 Mol:0
143: [06:34:56] Rep: launch :0 Mol:1
143: [06:34:56] Rep: 0 Mol:5
143: [06:34:56] Rep: 0 Mol:9
143: [06:34:56] Rep: 0 Mol:2
143: [06:34:56] Rep: 0 Mol:4
143: 3
159: Done
159: ----------------- Test 7 (backgrounds)
143: [06:34:56] Rep: 0 Mol:3
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
161: file rxn_test1_4.png gave hash 1178565194U not the expected 1766700542U
126: Warning: Atom Count for residue ARG64A does not match expected count
160: file testGithub3226_2.png gave hash 1415443727U not the expected 643975155U
159: file test7_1.png gave hash 37955190U not the expected 1322246680U
143: [06:34:56] Rep: 0 Mol:13
143: [06:34:56] Rep: 0 Mol:8
143: [06:34:56] Rep: 0 Mol:6
143: [06:34:56] Rep: 0 Mol:12
158: .
158: ----------------------------------------------------------------------
158: Ran 1 test in 0.025s
158:
158: OK
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
154: ..[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
143: [06:34:56] Rep: 0 Mol:16
143: [06:34:56] Rep: 0 Mol:17
159: file test7_2.png gave hash 280222352U not the expected 1499012715U
159: Done
159: ----------------- Test8: PrepareMolDrawing
154: .[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
159: Done
159: ----------------- Test multi-threaded drawing
159: reading molecules
143: [06:34:56] Rep: 0 Mol:10
154: .[06:34:56] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ]
154: [06:34:56] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]'
143: [06:34:56] Rep: 0 Mol:20
154: ...
154: ----------------------------------------------------------------------
154: Ran 9 tests in 0.119s
154:
154: OK
143: [06:34:56] Rep: 0 Mol:24
161: file rxn_test1_5.png gave hash 2486693442U not the expected 2552100594U
160: file testGithub3226_3.png gave hash 2009594401U not the expected 3119571946U
143: [06:34:56] Rep: 0 Mol:28
143: [06:34:56] Rep: 0 Mol:7
143: [06:34:56] Rep: 0 Mol:11
130: [06:34:56] done
130: [06:34:56] -------------------------------------
130: [06:34:56] Test GitHub Issue #6958
130: [06:34:56] DEPRECATION WARNING: please use AtomPairGenerator
143: [06:34:56] Rep: 0 Mol:15
128/235 Test #130: testFingerprintGenerators .............. Passed 0.98 sec
test 170
Start 170: testRascalMCES
170: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES
170: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES
170: Test timeout computed to be: 1500
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
159: generating reference drawings
168:
168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1
168: Time elapsed 0.009295 seconds
168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1
168: 1: NOREF. Reference data NOT LISTED in test case.
143: [06:34:56] Rep: 0 Mol:21
143: [06:34:56] Rep: 0 Mol:19
168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1
168: 2: NOREF. Reference data NOT LISTED in test case.
168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2]
168: 3: NOREF. Reference data NOT LISTED in test case.
168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2]
168: 4: NOREF. Reference data NOT LISTED in test case.
168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2]
168: 5: NOREF. Reference data NOT LISTED in test case.
168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1]
168: 6: NOREF. Reference data NOT LISTED in test case.
168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1]
168: 7: NOREF. Reference data NOT LISTED in test case.
160: file testPNGMetadata_1.png gave hash 1215431680U not the expected 997629701U
143: [06:34:56] Rep: 0 Mol:14
168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3]
168: 8: NOREF. Reference data NOT LISTED in test case.
168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2]
168: 9: NOREF. Reference data NOT LISTED in test case.
168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3]
168: 10: NOREF. Reference data NOT LISTED in test case.
129/235 Test #158: pyMolCatalog ........................... Passed 0.40 sec
test 171
Start 171: testRascalCluster
171: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster
171: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES
171: Test timeout computed to be: 1500
143: [06:34:56] Rep: 0 Mol:23
143: [06:34:56] Rep: 0 Mol:27
143: [06:34:56] Rep: 0 Mol:31
168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2]
168: 11: NOREF. Reference data NOT LISTED in test case.
168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1]
168: 12: NOREF. Reference data NOT LISTED in test case.
168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2]
168: 13: NOREF. Reference data NOT LISTED in test case.
168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2]
168: 14: NOREF. Reference data NOT LISTED in test case.
168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1]
168: 15: NOREF. Reference data NOT LISTED in test case.
168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1]
168: 16: NOREF. Reference data NOT LISTED in test case.
168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1]
168: 17: NOREF. Reference data NOT LISTED in test case.
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
143: [06:34:56] Rep: 0 Mol:25
168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1]
168: 18: NOREF. Reference data NOT LISTED in test case.
143: [06:34:56] Rep: 0 Mol:18
143: [06:34:56] Rep: 0 Mol:29
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
168:
168: --- UNMATCHED Reference RESULTS: ---
168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1]
168: -----------------------------------
168: Time elapsed 0.004340 seconds
168:
168: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717
168: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O
168: 1: PASSED. matchedRefRes = 4
130/235 Test #154: pyChemicalFeatures ..................... Passed 0.48 sec
168: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2]
168: 2: PASSED. matchedRefRes = 1
143: [06:34:56] Rep: 0 Mol:22
test 172
Start 172: pyRascalMCES
172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py"
172: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap
172: Test timeout computed to be: 1500
168: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2]
168: 3: PASSED. matchedRefRes = 6
168: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2]
168: 4: PASSED. matchedRefRes = 13
143: [06:34:56] Rep: 0 Mol:26
161: file rxn_test1_6.png gave hash 3683203876U not the expected 3791582903U
168: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2]
168: 5: PASSED. matchedRefRes = 12
168: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1]
168: 6: PASSED. matchedRefRes = 10
168: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1]
168: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1]
168: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1]
168: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1]
168: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1]
168: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1]
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
168: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1]
168: 10: PASSED. matchedRefRes = 3
108: .......
108: ----------------------------------------------------------------------
108: Ran 21 tests in 1.067s
108:
108: OK
108: (Five aromatic carbons And (Not any of Five aromatic carbons))
108: (Five aromatic carbons Or (Not any of Five aromatic carbons))
108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons)))
108: ********************************************
108: Testing: PAINS_A 2
108: ********************************************
108: Testing: PAINS_B 4
108: ********************************************
108: Testing: PAINS_C 8
108: ********************************************
108: Testing: PAINS 14
108: (Not FilterMatcher)
108: Bar
108: Count 1
108: ********************************************
108: {'Cl,Br,I'}
108: 1
108: 2
108: running
168: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1]
168: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1]
160: file testPNGMetadata_2.png gave hash 421119850U not the expected 1797853056U
168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]
168: 12: PASSED. matchedRefRes = 8
168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1]
168: 13: PASSED. matchedRefRes = 9
168: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]
168: 14: PASSED. matchedRefRes = 11
143: [06:34:56] Rep: 0 Mol:30
168: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1]
168: 15: PASSED. matchedRefRes = 2
141: processing
141: launch :0
141: launch :1
141: launch :2
141: launch :3
141: [06:34:56] Rep: 0 Mol:3
141: [06:34:56] Rep: 0 Mol:0
141: [06:34:56] Rep: 0[06:34:56] Rep: 0 Mol:1
141: Mol:2
141: [06:34:56] Rep: 0 Mol:5
141: [06:34:56] Rep: 0 Mol:9
141: [06:34:56] Rep: 0 Mol:4
141: [06:34:56] Rep: 0 Mol:13
168:
168: --- UNMATCHED Reference RESULTS: ---
168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]
168: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2]
168: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]
168: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]
168: -----------------------------------
168:
168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717
168: Time elapsed 0.008558 seconds
168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O
168: 1: PASSED. matchedRefRes = 4
168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2]
168: 2: PASSED. matchedRefRes = 1
168: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2]
168: 3: PASSED. matchedRefRes = 6
168: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2]
168: 4: PASSED. matchedRefRes = 13
117: =>start test morse custom
117: [06:34:56] test on : 365 molecules done
167: ....
167: ----------------------------------------------------------------------
167: Ran 4 tests in 0.013s
167:
167: OK
141: [06:34:56] Rep: 0 Mol:8
168: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2]
168: 5: PASSED. matchedRefRes = 12
168: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1]
168: 6: PASSED. matchedRefRes = 10
168: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1]
168: 7: NOREF. Reference data NOT LISTED in test case.
168: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1]
168: 8: NOREF. Reference data NOT LISTED in test case.
168: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1]
168: 9: NOREF. Reference data NOT LISTED in test case.
168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1]
168: 10: PASSED. matchedRefRes = 3
159: processing
159: launch :0
141: [06:34:56] Rep: 0 Mol:7
168: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1]
168: 11: NOREF. Reference data NOT LISTED in test case.
159: launch :1
159: launch :2
141: [06:34:56] Rep: 0 Mol:12
141: [06:34:56] Rep: 0 Mol:11
159: launch :3
168: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]
168: 12: PASSED. matchedRefRes = 8
141: [06:34:56] Rep: 0 Mol:17
168: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1]
168: 13: PASSED. matchedRefRes = 9
141: [06:34:56] Rep: 0 Mol:15
168: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]
168: 14: PASSED. matchedRefRes = 11
141: [06:34:56] Rep: 0 Mol:16
141: [06:34:56] Rep: 0 Mol:6
168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1]
168: 15: PASSED. matchedRefRes = 2
141: [06:34:56] Rep: 0 Mol:19
161: file rxn_test1_7.png gave hash 1361790131U not the expected 1461397406U
168:
168: --- UNMATCHED Reference RESULTS: ---
168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]
168: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2]
168: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2]
168: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]
168: -----------------------------------
168:
168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE
168: Time elapsed 0.001183 seconds
168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1]
168: 1: PASSED. matchedRefRes = 2
168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1]
168: 2: PASSED. matchedRefRes = 3
168: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2]
168: 3: NOREF. Reference data NOT LISTED in test case.
168: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2]
168: 4: PASSED. matchedRefRes = 4
168: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1]
168: 5: PASSED. matchedRefRes = 5
168: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1]
168: 6: NOREF. Reference data NOT LISTED in test case.
141: [06:34:56] Rep: 0 Mol:23
168: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1]
168: 7: PASSED. matchedRefRes = 7
141: [06:34:56] Rep: 0 Mol:27
141: [06:34:56] Rep: 0 Mol:10
161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U
161: Done
161: ----------------- Test 2: some examples that caused problems in testing
168:
168: --- UNMATCHED Reference RESULTS: ---
168: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3]
168: 6: CC(N1CC1)C(=O),Case1-SIMPLE,CC([*:1])[*:2],C1CN1[*:1].O=C[*:2]
168: -----------------------------------
168:
168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1
168: Time elapsed 0.004923 seconds
168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1
168: 1: NOREF. Reference data NOT LISTED in test case.
141: [06:34:56] Rep: 0 Mol:31
168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1
168: 2: NOREF. Reference data NOT LISTED in test case.
141: [06:34:56] Rep: 0 Mol:20
168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2]
168: 3: NOREF. Reference data NOT LISTED in test case.
168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2]
168: 4: NOREF. Reference data NOT LISTED in test case.
168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2]
168: 5: NOREF. Reference data NOT LISTED in test case.
168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1]
168: 6: NOREF. Reference data NOT LISTED in test case.
168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1]
168: 7: NOREF. Reference data NOT LISTED in test case.
168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3]
168: 8: NOREF. Reference data NOT LISTED in test case.
168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2]
168: 9: NOREF. Reference data NOT LISTED in test case.
168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3]
168: 10: NOREF. Reference data NOT LISTED in test case.
168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2]
168: 11: NOREF. Reference data NOT LISTED in test case.
168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1]
168: 12: NOREF. Reference data NOT LISTED in test case.
156: .
156: ----------------------------------------------------------------------
156: Ran 1 test in 0.063s
156:
156: OK
156: Testing Shape Helpers wrapper
126: Warning: Atom Count for residue LYS80A does not match expected count
168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2]
168: 13: NOREF. Reference data NOT LISTED in test case.
168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2]
168: 14: NOREF. Reference data NOT LISTED in test case.
168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1]
168: 15: NOREF. Reference data NOT LISTED in test case.
168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1]
168: 16: NOREF. Reference data NOT LISTED in test case.
141: [06:34:56] Rep: 0 Mol:24
131/235 Test #167: pyMolHash .............................. Passed 0.31 sec
test 173
Start 173: testSynthonSpaceSubstructureSearch
173: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch
173: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch
173: Test timeout computed to be: 1500
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1]
168: 17: NOREF. Reference data NOT LISTED in test case.
168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1]
168: 18: NOREF. Reference data NOT LISTED in test case.
160: [06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
141: [06:34:56] Rep: 0 Mol:28
162: ...[06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Amadeus.ttf not found.
162: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
168:
168: --- UNMATCHED Reference RESULTS: ---
168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1]
168: -----------------------------------
168:
168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2
168: Time elapsed 0.005703 seconds
168: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1
168: 1: NOREF. Reference data NOT LISTED in test case.
168: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1
168: 2: NOREF. Reference data NOT LISTED in test case.
141: [06:34:56] Rep: 0 Mol:21
168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1
168: 3: NOREF. Reference data NOT LISTED in test case.
168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1
168: 4: NOREF. Reference data NOT LISTED in test case.
69: Test
69:
69: RxnNoCoords.mrv
69:
69: Test
69:
69: mrvValenceZero.mrv
69:
69: Test
69:
69: condition_coordinates_mpoint.mrv
69:
69: Test
69:
69: marvin01.mrv
69:
69: Test
69:
69: aspirineSynthesisWithAttributes.mrv
69:
69: Test
69:
69: marvin01.mrv
69:
69: Test
69:
69: NewChiralTest
69:
69: Test
69:
69: NewChiralTest
69:
69: Test
69:
69: NewChiralTestNoChiral
69:
69: Test
69:
69: NewChiralTestNoChiral
69:
69: Test
69:
69: NewChiralTest2
69:
69: Test
69:
69: NewChiralTest2
69:
69: Test
69:
69: NewChiralTest2AllChiral
69:
69: Test
69:
69: NewChiralTest2AllChiral
69:
69: Test
69:
69: Vendor839
69:
69: Test
69:
69: DoubleBondChain
69:
69: Test
69:
69: Na_Mg_Al_OH
69:
69: Test
69:
69: Pb
69:
69: Test
69:
69: O_Mg_Si
69:
69: Test
69:
69: SquiggleBond
69:
69: Test
69:
69: BigMacrocycle
69:
69: Test
69:
69: Smiles1
69:
168: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1
168: 5: NOREF. Reference data NOT LISTED in test case.
168: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1
168: 6: NOREF. Reference data NOT LISTED in test case.
132/235 Test #108: pyFilterCatalog ........................ Passed 1.52 sec
160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U
test 174
Start 174: testCIPLabeler
174: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler
174: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler
174: Test timeout computed to be: 1500
160: [06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
168: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1
168: 7: NOREF. Reference data NOT LISTED in test case.
168: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1
168: 8: NOREF. Reference data NOT LISTED in test case.
168: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1
168: 9: NOREF. Reference data NOT LISTED in test case.
168: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1
168: 10: NOREF. Reference data NOT LISTED in test case.
168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1
168: 11: NOREF. Reference data NOT LISTED in test case.
168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1]
168: 12: NOREF. Reference data NOT LISTED in test case.
168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2]
168: 13: NOREF. Reference data NOT LISTED in test case.
161: file rxn_test2_1.png gave hash 700636031U not the expected 3551633840U
133/235 Test #69: testMrvToMol ........................... Passed 1.69 sec
test 175
Start 175: pyCIPLabelsWrapTest
175: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py"
175: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap
175: Test timeout computed to be: 1500
168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1
168: 14: PASSED. matchedRefRes = 1
168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1
168: 15: NOREF. Reference data NOT LISTED in test case.
168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1]
168: 16: NOREF. Reference data NOT LISTED in test case.
168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1
168: 17: NOREF. Reference data NOT LISTED in test case.
168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1
168: 18: NOREF. Reference data NOT LISTED in test case.
168:
168: --- ALL PASSED ---
168: -----------------------------------
168: 5 TEST CASES FAILED
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
134/235 Test #168: testMMPA ............................... Passed 0.25 sec
141: [06:34:56] Rep: 0 Mol:25
test 176
Start 176: pyCIPLabelsValidation
176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py"
176: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap
176: Test timeout computed to be: 1500
160: file testHandDrawn-1.png gave hash 2810773836U not the expected 3894611804U
135/235 Test #156: pyShapeHelpers ......................... Passed 0.61 sec
test 177
Start 177: deprotectTest
177: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest
177: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect
177: Test timeout computed to be: 1500
141: [06:34:56] Rep: 0 Mol:29
161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C
141: [06:34:56] Rep: 0 Mol:14
161: file rxn_test2_2_1.png gave hash 766587530U not the expected 1268122583U
162: ..........[06:34:56]
162:
162: ****
141: [06:34:56] Rep: 0 Mol:18
162: Pre-condition Violation
162: molecule must not be None
162: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp
162: Failed Expression: m
162: ----------
162: Stacktrace:
162: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
162: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so
162: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDKit::ROMol* (*)(RDKit::ROMol const*, bool, bool, bool, bool, bool), boost::python::return_value_policy<boost::python::manage_new_object, boost::python::default_call_policies>, boost::mpl::vector7<RDKit::ROMol*, RDKit::ROMol const*, bool, bool, bool, bool, bool> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so
162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
162: 5# 0x00007F6E41E9162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
162: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
162: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
162: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
162: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
162: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
162: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
162: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
162: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
162: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
162: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
162: 16# 0x00007F6E405B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
162: 17# 0x00007F6E405B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
162: 18# 0x00007F6E405B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
162: 19# 0x00007F6E405B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
162: 20# 0x00007F6E405B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
162: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
162: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
162: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
162: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
162: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
162: 26# 0x00007F6E41E8E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
162: 27# _PyObject_MakeTpCall in /usr/bin/python3
162: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
162: 29# 0x00000000005BEE79 in /usr/bin/python3
162: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
162: 31# 0x0000000000547080 in /usr/bin/python3
162: 32# 0x00000000006AB720 in /usr/bin/python3
162: 33# _PyObject_MakeTpCall in /usr/bin/python3
162: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
162: 35# 0x00000000005BEE79 in /usr/bin/python3
162: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
162: 37# 0x0000000000547080 in /usr/bin/python3
162: 38# 0x00000000006AB720 in /usr/bin/python3
162: 39# _PyObject_MakeTpCall in /usr/bin/python3
162: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
162: 41# 0x00000000005BEE79 in /usr/bin/python3
162: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
162: 43# 0x0000000000547080 in /usr/bin/python3
162: 44# 0x00000000006AB720 in /usr/bin/python3
162: 45# _PyObject_MakeTpCall in /usr/bin/python3
162: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
162: 47# 0x000000000059582E in /usr/bin/python3
162: 48# _PyObject_MakeTpCall in /usr/bin/python3
162: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
162: 50# PyEval_EvalCode in /usr/bin/python3
162: 51# 0x000000000066A861 in /usr/bin/python3
162: 52# 0x000000000066670C in /usr/bin/python3
162: 53# 0x000000000067F713 in /usr/bin/python3
162: 54# 0x000000000067ECE3 in /usr/bin/python3
162: 55# 0x000000000067EB1E in /usr/bin/python3
162: 56# Py_RunMain in /usr/bin/python3
162: 57# Py_BytesMain in /usr/bin/python3
162: 58# 0x00007F6E430B7CA8 in /lib/x86_64-linux-gnu/libc.so.6
162: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
162: 60# _start in /usr/bin/python3
162: ----------
162: ****
162:
161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
174: Randomness seeded to: 21943762
174: [06:34:56] non kekulizable aromatic bond being treated as bond order 1
174: [06:34:56] non kekulizable aromatic bond being treated as bond order 1
174: [06:34:56] non kekulizable aromatic bond being treated as bond order 1
174: [06:34:56] non kekulizable aromatic bond being treated as bond order 1
174: [06:34:56] non kekulizable aromatic bond being treated as bond order 1
174: [06:34:56] non kekulizable aromatic bond being treated as bond order 1
141: [06:34:56] Rep: 0 Mol:22
161: file rxn_test2_2_2.png gave hash 1252117625U not the expected 82821108U
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
161: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C
161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl
161: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C
160: [06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
141: [06:34:56] Rep: 0 Mol:26
89: [06:34:56] Explicit valence for atom # 9 N, 6, is greater than permitted
160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U
161: file rxn_test2_2_3.png gave hash 3797481496U not the expected 3828365604U
160: [06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
161: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC
141: [06:34:56] Rep: 0 Mol:30
70: [06:34:56] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas
70: [06:34:56] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas'
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
160: file testHandDrawn-2.png gave hash 3255836690U not the expected 1443443188U
160: [06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U
160: [06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
161: file rxn_test2_2_4.png gave hash 1813989566U not the expected 1230108677U
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
160: file testHandDrawn-3.png gave hash 1999104941U not the expected 865629432U
161: Done
161: ----------------- Test 3: test reactant highlighting
160: [06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U
160: [06:34:56] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:56] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
177: Randomness seeded to: 836248349
177: ===============================================================================
177: All tests passed (111 assertions in 3 test cases)
177:
136/235 Test #177: deprotectTest .......................... Passed 0.17 sec
test 178
Start 178: pyDeprotect
178: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap/rough_test.py"
178: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap
178: Test timeout computed to be: 1500
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
160: file testHandDrawn-4.png gave hash 1317783250U not the expected 3919767093U
141: [06:34:56] Rep: 20 Mol:3
141: [06:34:56] Rep: 20 Mol:7
141: [06:34:56] Rep: 20 Mol:11
141: [06:34:56] Rep: 20 Mol:15
141: [06:34:56] Rep: 20 Mol:19
141: [06:34:56] Rep: 20 Mol:23
141: [06:34:56] Rep: 20 Mol:27
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
141: [06:34:56] Rep: 20 Mol:31
161: file rxn_test3_1.png gave hash 887759826U not the expected 4189980366U
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
70: [06:34:56] Empty atom list: 'M ALS 1 0 F' on line 8.
161: Done
161: ----------------- Test 4: some examples from SMARTS in testing
161: draw!
70: de_DE.UTF-8
70: [06:34:56] -------------------------------------
70: [06:34:56] Test multithreading Locale Switching
148: [06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
141: [06:34:56] Rep: 20 Mol:0
141: [06:34:56] Rep: 20 Mol:4
141: [06:34:56] Rep: 20 Mol:8
141: [06:34:56] Rep: 20 Mol:12
141: [06:34:56] Rep: 20 Mol:16
162: ......................
162: ----------------------------------------------------------------------
162: Ran 35 tests in 0.329s
162:
162: OK
162: json lasso
148: .[06:34:56] Molecule does not have explicit Hs. Consider calling AddHs()
141: [06:34:56] Rep: 20 Mol:20
141: [06:34:56] Rep: 20 Mol:24
141: [06:34:56] Rep: 20 Mol:28
117: =>start test AUTOCORR3D custom
117: [06:34:57] test on : 365 molecules done
89: [06:34:57] Explicit valence for atom # 3 Al, 6, is greater than permitted
175: ....
175: ----------------------------------------------------------------------
175: Ran 4 tests in 0.026s
175:
175: OK
70: [06:34:57] Test multithreading (Done)
70: [06:34:57] -------------------------------------
161: file rxn_test4_1.png gave hash 2871076982U not the expected 2745201873U
161: done
137/235 Test #175: pyCIPLabelsWrapTest .................... Passed 0.38 sec
test 179
Start 179: testReducedGraphs
179: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs
179: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs
179: Test timeout computed to be: 1500
141: [06:34:57] Rep: 20 Mol:1
141: [06:34:57] Rep: 20 Mol:5
141: [06:34:57] Rep: 20 Mol:9
70: ***************************************
70: ***************************************
141: [06:34:57] Rep: 20 Mol:13
141: [06:34:57] Rep: 20 Mol:17
141: [06:34:57] Rep: 20 Mol:21
141: [06:34:57] Rep: 20 Mol:25
125: Warning: Atom Count for residue GLU150A does not match expected count
70: [06:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
70: [06:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
141: [06:34:57] Rep: 20 Mol:29
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
174: [06:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
174: [06:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored
179:
70: [06:34:57] bond with order 0 found on line 7. This is not part of the MDL specification.
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
179:
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
179:
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
179:
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
179:
89: [06:34:57] Explicit valence for atom # 4 Al, 6, is greater than permitted
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
179:
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
179:
138/235 Test #162: pyMolDraw2D ............................ Passed 0.86 sec
test 180
Start 180: pyReducedGraphs
180: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py"
180: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap
180: Test timeout computed to be: 1500
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
179:
179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ]
179:
70: [06:34:57] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7)
70: [06:34:57] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7)
70: [06:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
161: file rxn_test4_2.png gave hash 424710428U not the expected 3094925886U
139/235 Test #179: testReducedGraphs ...................... Passed 0.06 sec
test 181
Start 181: trajectoryTest
181: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest
181: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory
181: Test timeout computed to be: 1500
161: Done
70: generating smiles
125: Warning: Atom Count for residue ASN157A does not match expected count
140/235 Test #161: moldraw2DRxnTest1 ...................... Passed 0.95 sec
70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2
70: converting back
test 182
Start 182: substructLibraryTest
182: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest
182: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary
182: Test timeout computed to be: 1500
89: [06:34:57] Explicit valence for atom # 10 Si, 6, is greater than permitted
70: check isomorphism
174: ===============================================================================
174: All tests passed (6577 assertions in 19 test cases)
174:
141/235 Test #174: testCIPLabeler ......................... Passed 0.49 sec
test 183
Start 183: substructLibraryCatchTest
183: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest
183: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary
183: Test timeout computed to be: 1500
141: [06:34:57] Rep: 40 Mol:3
141: [06:34:57] Rep: 40 Mol:7
141: [06:34:57] Rep: 40 Mol:11
141: [06:34:57] Rep: 40 Mol:15
141: [06:34:57] Rep: 40 Mol:19
141: [06:34:57] Rep: 40 Mol:23
141: [06:34:57] Rep: 40 Mol:27
141: [06:34:57] Rep: 40 Mol:31
182: [06:34:57] -------------------------------------
182: [06:34:57] Test1
141: [06:34:57] Rep: 20 Mol:2
141: [06:34:57] Rep: 20 Mol:6
141: [06:34:57] Rep: 20 Mol:10
141: [06:34:57] Rep: 20 Mol:14
141: [06:34:57] Rep: 20 Mol:18
141: [06:34:57] Rep: 20 Mol:22
141: [06:34:57] Rep: 20 Mol:26
141: [06:34:57] Rep: 20 Mol:30
126: Warning: Atom Count for residue GLU150A does not match expected count
148: [06:34:57] Molecule does not have explicit Hs. Consider calling AddHs()
117: =>start test 2 WHIM custom
117: [06:34:57] test on : 365 molecules done
143: [06:34:57] Rep: 100 Mol:0
143: [06:34:57] Rep: 100 Mol:4
143: [06:34:57] Rep: 100 Mol:8
143: [06:34:57] Rep: 100 Mol:12
143: [06:34:57] Rep: 100 Mol:16
143: [06:34:57] Rep: 100 Mol:3
143: [06:34:57] Rep: 100 Mol:7
143: [06:34:57] Rep: 100 Mol:11
143: [06:34:57] Rep: 100 Mol:15
143: [06:34:57] Rep: 100 Mol:19
143: [06:34:57] Rep: 100 Mol:23
143: [06:34:57] Rep: 100 Mol:27
143: [06:34:57] Rep: 100 Mol:31
143: [06:34:57] Rep: 100 Mol:20
143: [06:34:57] Rep: 100 Mol:24
143: [06:34:57] Rep: 100 Mol:28
126: Warning: Atom Count for residue ASN157A does not match expected count
178: .....
178: ----------------------------------------------------------------------
178: Ran 5 tests in 0.098s
178:
178: OK
178: Testing tert-butyldimethylsilyl
178: Testing methoxytrityl
178: Testing tetrahydropyranyl
178: Testing methoxymethyl_ether
178: Testing beta-Methoxyethoxymethyl_ether
178: Testing benzyl
178: Testing trimethylsilyl
178: Testing benzoyl
178: Testing pivaloyl
178: Testing triisopropylsilyl
178: Testing acetyl
178: Testing para-methoxybenzyl_ether
178: Testing triphenylmethyl
178: Testing phthaloyl
178: Testing trimethylsilylethoxymethyl
178: Testing para-methoxyphenyl
178: Testing tosyl
178: Testing tert-butyloxycarbonyl
178: Testing trifluoroacetyl
178: Testing benzoyl
178: Testing 9-fluorenylmethyloxycarbonyl
178: Testing benzylamine
178: Testing acetamide
178: Testing carbobenzyloxy
178: Testing Acetal/Ketal
178: Testing tert-butyldimethylsilyl
178: Testing methoxytrityl
178: Testing tetrahydropyranyl
178: Testing methoxymethyl_ether
178: Testing beta-Methoxyethoxymethyl_ether
178: Testing benzyl
178: Testing trimethylsilyl
178: Testing benzoyl
178: Testing pivaloyl
178: Testing triisopropylsilyl
178: Testing acetyl
178: Testing para-methoxybenzyl_ether
178: Testing triphenylmethyl
178: Testing phthaloyl
178: Testing trimethylsilylethoxymethyl
178: Testing para-methoxyphenyl
178: Testing tosyl
178: Testing tert-butyloxycarbonyl
178: Testing trifluoroacetyl
178: Testing benzoyl
178: Testing 9-fluorenylmethyloxycarbonyl
178: Testing benzylamine
178: Testing acetamide
178: Testing carbobenzyloxy
178: Testing Acetal/Ketal
141: [06:34:57] Rep: 40 Mol:0
141: [06:34:57] Rep: 40 Mol:4
141: [06:34:57] Rep: 40 Mol:8
141: [06:34:57] Rep: 40 Mol:12
141: [06:34:57] Rep: 40 Mol:16
141: [06:34:57] Rep: 40 Mol:20
141: [06:34:57] Rep: 40 Mol:24
141: [06:34:57] Rep: 60 Mol:3
141: [06:34:57] Rep: 40 Mol:28
141: [06:34:57] Rep: 60 Mol:7
141: [06:34:57] Rep: 60 Mol:11
141: [06:34:57] Rep: 60 Mol:15
141: [06:34:57] Rep: 60 Mol:19
141: [06:34:57] Rep: 60 Mol:23
141: [06:34:57] Rep: 60 Mol:27
141: [06:34:57] Rep: 60 Mol:31
172: ..........[06:34:57] Too many matching bond pairs (1032) so can't continue.
142/235 Test #178: pyDeprotect ............................ Passed 0.52 sec
89: [06:34:57] Explicit valence for atom # 2 O, 4, is greater than permitted
89: [06:34:57] Explicit valence for atom # 3 Al, 6, is greater than permitted
89: [06:34:57] Explicit valence for atom # 3 Be, 4, is greater than permitted
89: [06:34:57] Explicit valence for atom # 27 P, 6, is greater than permitted
147: [06:34:57] UFFTYPER: Warning: hybridization set to SP3 for atom 6
147: [06:34:57] UFFTYPER: Warning: hybridization set to SP3 for atom 6
147: [06:34:57] UFFTYPER: Warning: hybridization set to SP3 for atom 6
180: .....
180: ----------------------------------------------------------------------
180: Ran 5 tests in 0.017s
180:
180: OK
143: [06:34:57] Rep: 100 Mol:1
143: [06:34:57] Rep: 100 Mol:5
143: [06:34:57] Rep: 100 Mol:9
143: [06:34:57] Rep: 100 Mol:13
143: [06:34:57] Rep: 100 Mol:17
143: [06:34:57] Rep: 100 Mol:21
143: [06:34:57] Rep: 100 Mol:25
143: [06:34:57] Rep: 100 Mol:29
146: [06:34:55] ---------------------------------
146: [06:34:55] test3
146:
146: [06:34:55] ---------------------------------
146: [06:34:55] test4
146:
146: [06:34:55] ---------------------------------
146: [06:34:55] test5
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test6
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test15Dists
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test Issue 215
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testMultipleConfs
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testMultipleConfsExpTors
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testIssue227
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testIssue236
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testOrdering
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testIssue244
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testIssue251
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testIssue276
146: [06:34:57] ---------------------------------
146: [06:34:57] testIssue284
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testIssue285
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testIssue355
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] testRandomCoords
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test sf.net issue 1989539
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test sf.net issue 2091864
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test constrained embedding
146:
146: [06:34:57] ssd: 0.0752641
146: [06:34:57] ssd: 0.0659363
141: [06:34:57] Rep: 40 Mol:1
141: [06:34:57] Rep: 40 Mol:5
141: [06:34:57] Rep: 40 Mol:9
141: [06:34:57] Rep: 40 Mol:13
141: [06:34:57] Rep: 40 Mol:17
141: [06:34:57] Rep: 40 Mol:21
141: [06:34:57] Rep: 40 Mol:25
141: [06:34:57] Rep: 40 Mol:29
148: [06:34:57] Molecule does not have explicit Hs. Consider calling AddHs()
test 184
Start 184: pySubstructLibrary
184: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py"
184: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap
184: Test timeout computed to be: 1500
143/235 Test #180: pyReducedGraphs ........................ Passed 0.44 sec
test 185
Start 185: testRGroupDecomp
185: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp
185: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition
185: Test timeout computed to be: 1500
182: [06:34:57] done
89: ===============================================================================
89: All tests passed (21562 assertions in 3 test cases)
89:
144/235 Test #89: multithreadedSupplierCatchTest ......... Passed 2.52 sec
test 186
Start 186: testRGroupDecompInternals
186: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals
186: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition
186: Test timeout computed to be: 1500
182: [06:34:57] -------------------------------------
182: [06:34:57] Test2
145/235 Test #181: trajectoryTest ......................... Passed 0.46 sec
test 187
Start 187: rgroupCatchTests
187: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests
187: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition
187: Test timeout computed to be: 1500
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
186: [06:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors
146/235 Test #186: testRGroupDecompInternals .............. Passed 0.05 sec
test 188
Start 188: pyRGroupDecomposition
188: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py"
188: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap
188: Test timeout computed to be: 1500
141: [06:34:57] Rep: 80 Mol:3
141: [06:34:57] Rep: 80 Mol:7
141: [06:34:57] Rep: 80 Mol:11
141: [06:34:57] Rep: 80 Mol:15
141: [06:34:57] Rep: 80 Mol:19
141: [06:34:57] Rep: 80 Mol:23
141: [06:34:57] Rep: 80 Mol:27
141: [06:34:57] Rep: 80 Mol:31
147: [06:34:57] UFFTYPER: Warning: hybridization set to SP3 for atom 11
183: Randomness seeded to: 3117864534
183: ===============================================================================
183: All tests passed (171 assertions in 5 test cases)
183:
147/235 Test #183: substructLibraryCatchTest .............. Passed 0.54 sec
test 189
Start 189: molInterchangeTest1
189: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1
189: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange
189: Test timeout computed to be: 1500
147: [06:34:57] UFFTYPER: Warning: hybridization set to SP3 for atom 11
148: [06:34:57] Molecule does not have explicit Hs. Consider calling AddHs()
189: [06:34:57] test1: basics
147: [06:34:57] UFFTYPER: Warning: hybridization set to SP3 for atom 11
141: [06:34:57] Rep: 40 Mol:2
141: [06:34:57] Rep: 40 Mol:6
141: [06:34:57] Rep: 40 Mol:10
141: [06:34:57] Rep: 40 Mol:14
117: =>start test 1 WHIM custom
117: [06:34:57] test on : 365 molecules done
141: [06:34:57] Rep: 40 Mol:18
141: [06:34:57] Rep: 40 Mol:22
141: [06:34:57] Rep: 40 Mol:26
141: [06:34:57] Rep: 40 Mol:30
189: [06:34:57] done
189: [06:34:57] test2: basic writing
189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,0]}]}]}
189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]}
189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]}
189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]}
189: [06:34:57] done
189: [06:34:57] test3: writing conformers
189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.6","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]}
189: [06:34:57] done
189: [06:34:57] test4: writing properties
189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,0]}]}]}
189: [06:34:57] done
189: [06:34:57] test5: writing partial charges
189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.6","values":[0.5,-0.5]}]}]}
189: [06:34:57] testing parse options
189: [06:34:57] done
189: [06:34:57] testing github #2046: CIPRank values from JSONDataToMols are not unsigned
189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]}
189: [06:34:57] done
189: [06:34:57] testing 'either' stereochemistry
189: [06:34:57] done
148/235 Test #189: molInterchangeTest1 .................... Passed 0.07 sec
test 190
Start 190: molInterchangeCatchTest
190: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest
190: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange
190: Test timeout computed to be: 1500
141: [06:34:57] Rep: 60 Mol:0
141: [06:34:57] Rep: 60 Mol:4
141: [06:34:57] Rep: 60 Mol:8
141: [06:34:57] Rep: 60 Mol:12
141: [06:34:57] Rep: 60 Mol:16
141: [06:34:57] Rep: 60 Mol:20
141: [06:34:57] Rep: 60 Mol:24
141: [06:34:57] Rep: 60 Mol:28
143: [06:34:57] Rep: 100 Mol:2
190: Randomness seeded to: 1956201749
190: [06:34:57] unrecognized bond type 12 set to zero while writing
190: [06:34:57] unrecognized bond type 0 set to zero while writing
143: [06:34:57] Rep: 100 Mol:6
143: [06:34:57] Rep: 100 Mol:10
143: [06:34:57] Rep: 100 Mol:14
143: [06:34:57] Rep: 100 Mol:18
143: [06:34:57] Rep: 100 Mol:22
143: [06:34:57] Rep: 100 Mol:26
190: ===============================================================================
190: All tests passed (125 assertions in 7 test cases)
190:
151: 1595152381
143: [06:34:57] Rep: 100 Mol:30
149/235 Test #190: molInterchangeCatchTest ................ Passed 0.09 sec
test 191
Start 191: pyMolInterchange
191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py"
191: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap
191: Test timeout computed to be: 1500
146: [06:34:57] ---------------------------------
146: [06:34:57] test sf.net issue 2091974
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test sf.net issue 2835784
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test sf.net issue 3019283
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test sf.net issue 3238580
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test sf.net issue 3483968
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test github issue 55
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test1
146:
146: [06:34:57] ---------------------------------
146: [06:34:57] test multi-threading
146:
98: .
98: ----------------------------------------------------------------------
98: Ran 11 tests in 2.497s
98:
98: OK
98: True
98: == CartesianProductStrategy CartesianProductStrategy
98: 197 out of 300
98: 0 6 out of 10
98: 1 3 out of 5
98: 2 4 out of 6
98: 198 out of 300
98: 0 10 out of 10
98: 1 5 out of 5
98: 2 6 out of 6
98: <rdkit.Chem.rdChemReactions.CartesianProductStrategy object at 0x7ff7aaf1dad0> Skipped 10000000 in 0.08902597427368164 seconds
98: <rdkit.Chem.rdChemReactions.RandomSampleStrategy object at 0x7ff7aaf1da30> Skipped 10000000 in 0.9402072429656982 seconds
98: <rdkit.Chem.rdChemReactions.RandomSampleAllBBsStrategy object at 0x7ff7aaf1d940> Skipped 10000000 in 1.1175084114074707 seconds
146: building molecules
146: generating reference data
141: [06:34:57] Rep: 60 Mol:1
141: [06:34:57] Rep: 60 Mol:5
141: [06:34:57] Rep: 60 Mol:9
185: [06:34:57] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters
141: [06:34:58] Rep: 60 Mol:13
141: [06:34:58] Rep: 60 Mol:17
141: [06:34:58] Rep: 60 Mol:21
141: [06:34:58] Rep: 60 Mol:25
185: [06:34:58] WARNING: not removing hydrogen atom with dummy atom neighbors
141: [06:34:58] Rep: 60 Mol:29
182: [06:34:58] done
41: [06:34:58] done: 500000
41: [06:34:58] Done
187: Randomness seeded to: 3095064553
187: ===============================================================================
187: All tests passed (1475 assertions in 14 test cases)
187:
150/235 Test #187: rgroupCatchTests ....................... Passed 0.42 sec
182: [06:34:58] -------------------------------------
182: [06:34:58] Test3 (stereo options)
148: [06:34:58] Molecule does not have explicit Hs. Consider calling AddHs()
test 192
Start 192: testSLNParse
192: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse
192: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse
192: Test timeout computed to be: 1500
141: [06:34:58] Rep: 60 Mol:2
151/235 Test #98: pyChemReactionEnumerations ............. Passed 2.97 sec
141: [06:34:58] Rep: 60 Mol:6
141: [06:34:58] Rep: 60 Mol:10
test 193
Start 193: pySLNParse
193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap/testSLN.py"
193: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap
193: Test timeout computed to be: 1500
141: [06:34:58] Rep: 60 Mol:14
141: [06:34:58] Rep: 60 Mol:18
141: [06:34:58] Rep: 60 Mol:22
141: [06:34:58] Rep: 60 Mol:26
141: [06:34:58] Rep: 60 Mol:30
41: [06:34:58] Testing hanoi with a functor.
192: Atoms:
192: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb:
192: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb:
192: 2 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb:
192: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb:
192: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb:
192: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb:
192: Bonds:
192: 0 0->1 order: 1
192: 1 0->2 order: 1
192: 2 0->3 order: 1
192: 3 0->4 order: 1
192: 4 0->5 order: 1
192: [06:34:58] SLN Parse Error: syntax error while parsing: CH4[I=13]
192: [06:34:58] Failed parsing SLN 'CH4[I=13]'
41: [06:34:58] Done
41: [06:34:58] Testing basic partition refinement.
41: [06:34:58] Done
41: [06:34:58] Testing partition refinement with neighbors.
41: [06:34:58] Done
41: [06:34:58] testing canonicalization via tie breaking.
41: [06:34:58] Done
41: [06:34:58] testing canonicalization using the wrapper.
192: [06:34:58] SLN Parser error: Atom ID 1 appears *after* its ring closure.
192: [06:34:58] SLN Parser error: Ring closure 1 does not have a corresponding opener.
192: [06:34:58] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2)
192: [06:34:58] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)'
192: [06:34:58] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1)
192: [06:34:58] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)'
192: [06:34:58] SLN Parse Error: syntax error while parsing: CH4 fff
192: [06:34:58] Failed parsing SLN 'CH4 fff'
192: [06:34:58] SLN Parse Error: syntax error while parsing: C[charge=+1] foo
192: [06:34:58] Failed parsing SLN 'C[charge=+1] foo'
192: [06:34:58] Query property 'is' ignored on non-query atom
192: [06:34:58] Query property 'is' ignored on non-query atom
152/235 Test #192: testSLNParse ........................... Passed 0.08 sec
test 194
Start 194: pyGraphMolWrap
194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rough_test.py"
194: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap
194: Test timeout computed to be: 1500
122: =>start test GETAWAY
122: [06:34:58] test on : 365 molecules done
153/235 Test #122: testGETAWAY ............................ Passed 2.82 sec
test 195
Start 195: pyTestConformerWrap
195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testConformer.py"
195: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap
195: Test timeout computed to be: 1500
160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U
160: [06:34:58] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
160: [06:34:58] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
41: [06:34:58] Done
41: [06:34:58] testing some specific ordering problems
41: [06:34:58] Finished
41: [06:34:58] testing chiral invariants.
41: [06:34:58] Finished
41: [06:34:58] testing unique ranks in w.r.t. renumbering.
148: [06:34:58] Molecule does not have explicit Hs. Consider calling AddHs()
160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U
160: [06:34:58] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found.
141: [06:34:58] Rep: 80 Mol:0
160: [06:34:58] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf.
141: [06:34:58] Rep: 80 Mol:4
141: [06:34:58] Rep: 80 Mol:8
191: ..
191: ----------------------------------------------------------------------
191: Ran 2 tests in 0.025s
191:
191: OK
141: [06:34:58] Rep: 80 Mol:12
141: [06:34:58] Rep: 80 Mol:16
141: [06:34:58] Rep: 80 Mol:20
141: [06:34:58] Rep: 80 Mol:24
141: [06:34:58] Rep: 80 Mol:28
182: [06:34:58] Done (stereo options)
182: [06:34:58] -------------------------------------
182: [06:34:58] Test4 (trusted smiles)
154/235 Test #191: pyMolInterchange ....................... Passed 0.41 sec
test 196
Start 196: pyTestTrajectory
196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testTrajectory.py"
196: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap
196: Test timeout computed to be: 1500
160: file testHandDrawn-5.png gave hash 2537746017U not the expected 828378555U
41: [06:34:58] Finished
41: [06:34:58] testing mol fragments.
41: [06:34:58] Finished
41: [06:34:58] testing protein round-tripping.
141: [06:34:58] Rep: 80 Mol:1
141: [06:34:58] Rep: 80 Mol:5
141: [06:34:58] Rep: 80 Mol:9
141: [06:34:58] Rep: 80 Mol:13
141: [06:34:58] Rep: 80 Mol:17
141: [06:34:58] Rep: 80 Mol:21
141: [06:34:58] Rep: 80 Mol:25
141: [06:34:58] Rep: 80 Mol:29
141: [06:34:58] Rep: 80 Mol:2
141: [06:34:58] Rep: 80 Mol:6
141: [06:34:58] Rep: 80 Mol:10
182: [06:34:58] Done (trusted smiles)
182: [06:34:58] -------------------------------------
182: [06:34:58] Testing C++ docs
182: [06:34:58] Done (C++ doc tests)
182: [06:34:58] -------------------------------------
182: [06:34:58] Testing C++ ring query: PatternHolder
141: [06:34:58] Rep: 80 Mol:14
182: [06:34:58] Done (C++ ring query tests)
182: [06:34:58] -------------------------------------
182: [06:34:58] Testing C++ ring query: TautomerPatternHolder
182: [06:34:58] Done (C++ ring query tests)
182: [06:34:58] -------------------------------------
182: [06:34:58] Add Patterns
141: [06:34:58] Rep: 80 Mol:18
141: [06:34:58] Rep: 80 Mol:22
141: [06:34:58] Rep: 80 Mol:26
141: [06:34:58] Rep: 80 Mol:30
151: 518518365
151: ===============================================================================
151: All tests passed (73 assertions in 3 test cases)
151:
155/235 Test #151: molAlignCatchTest ...................... Passed 2.36 sec
test 197
Start 197: pyTestSGroups
197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testSGroups.py"
197: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap
197: Test timeout computed to be: 1500
173: Randomness seeded to: 575041804
173: [06:34:58] Writing the enumerated file may take quite some time and result in a large file.
160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U
193: ..
193: ----------------------------------------------------------------------
193: Ran 2 tests in 0.012s
193:
193: OK
156/235 Test #193: pySLNParse ............................. Passed 0.50 sec
test 198
Start 198: pyTestThreads
198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testThreads.py"
198: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap
198: Test timeout computed to be: 1500
160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U
195: ......
195: ----------------------------------------------------------------------
195: Ran 6 tests in 0.020s
195:
195: OK
157/235 Test #195: pyTestConformerWrap .................... Passed 0.46 sec
test 199
Start 199: pyTestMultithreadedMolSupplier
199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py"
199: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap
199: Test timeout computed to be: 1500
160: [06:34:58] unrecognized bond typefile testGithub4238_1.png gave hash 1999044295U not the expected 2623427676U
160: file testGithub4323_1.png gave hash 1674734291U not the expected 3075787867U
143: [06:34:58] done
143: [06:34:58] -------------------------------------
143: [06:34:58] Test UFF multithreading2
158/235 Test #43: resMolSupplierTest ..................... Passed 3.92 sec
test 200
Start 200: pyTestPropertyLists
200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testPropertyLists.py"
200: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap
200: Test timeout computed to be: 1500
141: [06:34:58] done
141: [06:34:58] -------------------------------------
141: [06:34:58] Test MMFF multithreading2
29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log...
194: ..............[06:34:58] SMARTS Parse Error: syntax error while parsing: fiib
194: [06:34:58] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib'
163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds
163: Time elapsed 0.005 seconds
163:
163: test32()
163: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds
163: Time elapsed 0.087 seconds
163:
163: test190()
163: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds
163: Time elapsed 0.009 seconds
163:
163: test3()
163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds
163: Time elapsed 0.015 seconds
163:
163: testSimpleFast()
163: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds
163: Time elapsed 0.146 seconds
163:
163: testSimple()
163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds
163: Time elapsed 0.185 seconds
163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds
163: Time elapsed 0.127 seconds
163: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds
163: Time elapsed 0.173 seconds
163:
163: testSegFault()
163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds
163: Time elapsed 0.013 seconds
163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds
163: Time elapsed 0.039 seconds
163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds
163: Time elapsed 0.039 seconds
163:
163: testThreshold()
163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds
163: Time elapsed 0.000 seconds
163:
163: testRing1()
163: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds
163: Time elapsed 0.739 seconds
163: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds
163: Time elapsed 0.557 seconds
163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds
163: Time elapsed 0.393 seconds
163:
163: testAtomCompareIsotopes()
163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds
163: Time elapsed 0.000 seconds
163:
163: testAtomCompareAnyAtom()
163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds
163: Time elapsed 0.000 seconds
163:
163: testAtomCompareAnyAtom()
163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds
163: Time elapsed 0.000 seconds
163:
163: testAtomCompareAnyAtom()
163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds
163: Time elapsed 0.000 seconds
163:
163: testAtomCompareAnyAtom()
163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds
163: Time elapsed 0.000 seconds
163:
163: testJnk1LigandsDistance()
163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds
163: Time elapsed 0.009 seconds
163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds
194: ....[06:34:58] ERROR: Problems encountered parsing data fields
194: [06:34:59] ERROR: moving to the beginning of the next molecule
194: [06:34:59] ERROR: Problems encountered parsing data fields
194: [06:34:59] ERROR: moving to the beginning of the next molecule
194: [06:34:59] Spurious data before the first property will be ignored
194: [06:34:59] Property <ID> will be truncated after the first blank line
194: [06:34:59] Property <ID> will be truncated after the first blank line
194: [06:34:59] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
194: [06:34:59] ERROR: Problems encountered parsing data fields
194: [06:34:59] ERROR: moving to the beginning of the next molecule
194: [06:34:59] ERROR: Problems encountered parsing data fields
194: [06:34:59] ERROR: moving to the beginning of the next molecule
194: [06:34:59] Spurious data before the first property will be ignored
194: [06:34:59] Property <ID> will be truncated after the first blank line
194: [06:34:59] Property <ID> will be truncated after the first blank line
194: [06:34:59] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
194: [06:34:59] ERROR: Problems encountered parsing data fields
194: [06:34:59] ERROR: moving to the beginning of the next molecule
194: [06:34:59] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
194: [06:34:59] ERROR: Problems encountered parsing data fields
194: [06:34:59] ERROR: moving to the beginning of the next molecule
194: [06:34:59] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
194: .[06:34:59] SMILES Parse Error: syntax error while parsing: fail
194: [06:34:59] SMILES Parse Error: check for mistakes around position 1:
194: [06:34:59] fail
194: [06:34:59] ^
194: [06:34:59] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail'
194: [06:34:59] ERROR: Smiles parse error on line 2
194: [06:34:59] ERROR: Cannot create molecule from : 'fail'
194: >>> This may result in an infinite loop. It should finish almost instantly
194: <<< OK, it finished.
160: file testGithub4323_3.png gave hash 4270327094U not the expected 381907253U
160: [06:34:59] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered.
172: ....
172: ----------------------------------------------------------------------
172: Ran 14 tests in 2.040s
172:
172: OK
196: [06:34:59]
196:
196: ****
194: ............[06:34:59] Explicit valence for atom # 1 C, 5, is greater than permitted
196: Pre-condition Violation
196: from must be < size()
196: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: from < static_cast<int>(size())
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<unsigned int (RDKit::Trajectory::*)(RDKit::ROMol&, int, int), boost::python::default_call_policies, boost::mpl::vector5<unsigned int, RDKit::Trajectory&, RDKit::ROMol&, int, int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: .[06:34:59]
196:
196: ****
41: [06:34:59] Finished
41: [06:34:59] testing stability w.r.t. renumbering.
196: Pre-condition Violation
196: from must be < size()
196: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: from < static_cast<int>(size())
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<unsigned int (RDKit::Trajectory::*)(RDKit::ROMol&, int, int), boost::python::default_call_policies, boost::mpl::vector5<unsigned int, RDKit::Trajectory&, RDKit::ROMol&, int, int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
148: [06:34:59] Molecule does not have explicit Hs. Consider calling AddHs()
194: ......[06:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
194: [06:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
194: [06:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
194: [06:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
194: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)|
197: .............
197: ----------------------------------------------------------------------
197: Ran 13 tests in 0.065s
197:
197: OK
197: Testing SubstanceGroups wrapper
159/235 Test #172: pyRascalMCES ........................... Passed 2.53 sec
test 201
Start 201: pyCDXMLTest
201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/test_cdxml.py"
201: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap
201: Test timeout computed to be: 1500
163: Time elapsed 0.002 seconds
163:
163: test18()
163: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1
163: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds
163: Time elapsed 0.007 seconds
163:
163: test504()
163: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1
163: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds
163: Time elapsed 0.093 seconds
163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds
163: Time elapsed 0.001 seconds
163: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds
163: Time elapsed 0.028 seconds
163: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds
163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0011 seconds. bond[0]=6
163: STATISTICS:
163: Total Growing Steps = 1, MCS found on 1 step, for 0.0011 seconds
163: Initial Seeds = 1, Mismatched 0
163: Inspected Seeds = 2
163: Rejected by BestSize = 0
163: IndividualBondExcluded = 0
163: MatchCheck Seeds = 2
163: MatchCalls = 2
163: MatchFound = 1
163: fastMatchCalls = 1
163: fastMatchFound = 0
163: slowMatchCalls = 2
163: slowMatchFound = 1
163: DupCacheFound = 0 0 matched, 0 mismatched
163: HashCache size = 1 keys
163: HashCache size = 1 entries
163: FindHashInCache = 2
163: HashFoundInCache= 0
163: ExactMatchCalls = 0
163: ExactMatchFound = 0
163: Time elapsed 0.001 seconds
163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3
163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3
163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0
163: res sub = 1 size=3
163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds
163: test target = O[C@H](F)CCl query = C(F)C useChirality = 1
163: res sub = 1 size=3
163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds
163: test target = CC[C@H](F)Cl query = CCC useChirality = 0
163: res sub = 1 size=3
163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds
163: test target = CC[C@H](F)Cl query = CCC useChirality = 1
163: res sub = 1 size=3
163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds
163: test target = CCC(F)Cl query = CC useChirality = 0
163: res sub = 1 size=2
163: MCS: [#6]-[#6] 2 atoms, 1 bonds
163: test target = CCC(F)Cl query = CC useChirality = 1
163: res sub = 1 size=2
163: MCS: [#6]-[#6] 2 atoms, 1 bonds
163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0
163: res sub = 1 size=4
163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1
163: res sub = 1 size=4
163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0
163: res sub = 1 size=4
163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1
163: res sub = 1 size=4
163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0
163: res sub = 0 size=0
163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds
163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1
163: res sub = 0 size=0
163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds
163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1
163: res sub = 0 size=0
163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds
163: test target = OC(F)CCl query = OC(F)C useChirality = 0
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = OC(F)CCl query = OC(F)C useChirality = 1
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1
163: res sub = 0 size=0
163: MCS: [#9] 1 atoms, 0 bonds
163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0
163: res sub = 1 size=4
163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds
163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1
163: res sub = 0 size=0
163: MCS: [#9] 1 atoms, 0 bonds
163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0
163: res sub = 1 size=3
163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds
163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1
163: res sub = 1 size=3
163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds
163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0
163: res sub = 1 size=3
163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds
163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1
163: res sub = 1 size=3
163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds
163:
163: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>>
163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0
163: res sub = 1 size=3
163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds
163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1
163: res sub = 1 size=3
163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds
163: done
41: [06:34:59] Finished
41: [06:34:59] testing smiles round-tripping.
194: ........[06:34:59] non-ring atom 0 marked aromatic
194: [06:34:59] non-ring atom 0 marked aromatic
194: [06:34:59]
194:
194: ****
194: Range Error
194: idx
194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp
194: Failed Expression: 12 < 6
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 4# 0x00007F5673483170 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 26# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 28# _PyObject_MakeTpCall in /usr/bin/python3
194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 30# 0x00000000005BEE79 in /usr/bin/python3
194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 32# 0x0000000000547080 in /usr/bin/python3
194: 33# 0x00000000006AB720 in /usr/bin/python3
194: 34# _PyObject_MakeTpCall in /usr/bin/python3
194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 36# 0x00000000005BEE79 in /usr/bin/python3
194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 38# 0x0000000000547080 in /usr/bin/python3
194: 39# 0x00000000006AB720 in /usr/bin/python3
194: 40# _PyObject_MakeTpCall in /usr/bin/python3
194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 42# 0x00000000005BEE79 in /usr/bin/python3
194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 44# 0x0000000000547080 in /usr/bin/python3
194: 45# 0x00000000006AB720 in /usr/bin/python3
194: 46# _PyObject_MakeTpCall in /usr/bin/python3
194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 48# 0x000000000059582E in /usr/bin/python3
194: 49# _PyObject_MakeTpCall in /usr/bin/python3
194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 51# PyEval_EvalCode in /usr/bin/python3
194: 52# 0x000000000066A861 in /usr/bin/python3
194: 53# 0x000000000066670C in /usr/bin/python3
194: 54# 0x000000000067F713 in /usr/bin/python3
194: 55# 0x000000000067ECE3 in /usr/bin/python3
194: 56# 0x000000000067EB1E in /usr/bin/python3
194: 57# Py_RunMain in /usr/bin/python3
194: 58# Py_BytesMain in /usr/bin/python3
194: 59# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 61# _start in /usr/bin/python3
194: ----------
194: ****
194:
194: [06:34:59] non-ring atom 0 marked aromatic
194: [06:34:59] non-ring atom 0 marked aromatic
194: [06:34:59]
194:
194: ****
194: Range Error
194: idx
194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp
194: Failed Expression: 12 < 6
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 4# 0x00007F5673483170 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 26# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 28# _PyObject_MakeTpCall in /usr/bin/python3
194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 30# 0x00000000005BEE79 in /usr/bin/python3
194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 32# 0x0000000000547080 in /usr/bin/python3
194: 33# 0x00000000006AB720 in /usr/bin/python3
194: 34# _PyObject_MakeTpCall in /usr/bin/python3
194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 36# 0x00000000005BEE79 in /usr/bin/python3
194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 38# 0x0000000000547080 in /usr/bin/python3
194: 39# 0x00000000006AB720 in /usr/bin/python3
194: 40# _PyObject_MakeTpCall in /usr/bin/python3
194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 42# 0x00000000005BEE79 in /usr/bin/python3
194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 44# 0x0000000000547080 in /usr/bin/python3
194: 45# 0x00000000006AB720 in /usr/bin/python3
194: 46# _PyObject_MakeTpCall in /usr/bin/python3
194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 48# 0x000000000059582E in /usr/bin/python3
194: 49# _PyObject_MakeTpCall in /usr/bin/python3
194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 51# PyEval_EvalCode in /usr/bin/python3
194: 52# 0x000000000066A861 in /usr/bin/python3
194: 53# 0x000000000066670C in /usr/bin/python3
194: 54# 0x000000000067F713 in /usr/bin/python3
194: 55# 0x000000000067ECE3 in /usr/bin/python3
194: 56# 0x000000000067EB1E in /usr/bin/python3
194: 57# Py_RunMain in /usr/bin/python3
194: 58# Py_BytesMain in /usr/bin/python3
194: 59# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 61# _start in /usr/bin/python3
194: ----------
194: ****
194:
143: [06:34:59] done
143: [06:34:59] -------------------------------------
143: [06:34:59] Test UFF multithreading3
194: ...............[06:34:59] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count.
194: [06:34:59] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count.
148: [06:34:59] Molecule does not have explicit Hs. Consider calling AddHs()
199: .s.
199: ----------------------------------------------------------------------
199: Ran 3 tests in 0.186s
199:
199: OK (skipped=1)
199: Testing Smiles and SD MultithreadedMolSupplier
200: [06:34:59] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it.
200: [06:34:59] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it.
200: [06:34:59] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it.
200: .[06:34:59] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it.
200: [06:34:59] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it.
200: [06:34:59] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it.
200: ...[06:34:59] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it.
200: [06:34:59] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it.
200: [06:34:59] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it.
200: .
200: ----------------------------------------------------------------------
200: Ran 5 tests in 0.022s
200:
200: OK
194: ..............[06:34:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
194: [06:34:59] Explicit valence for atom # 1 C, 5, is greater than permitted
141: [06:34:59] done
141: [06:34:59] -------------------------------------
141: [06:34:59] Test MMFF multithreading3
41: [06:34:59] Finished
41: [06:34:59] testing github #1567: Non-canonical result from MolFragmentToSmiles()
41: [06:34:59] Finished
160/235 Test #41: hanoiTest .............................. Passed 4.43 sec
test 202
Start 202: molStandardizeTest
202: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest
202: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
202: Test timeout computed to be: 1500
70: [06:34:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored
70: [06:34:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored
70: [06:34:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored
70: [06:34:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored
70: [06:34:59] deprecated group abbreviation ignored on line 24
161/235 Test #197: pyTestSGroups .......................... Passed 0.85 sec
test 203
Start 203: molNormalizeTest
203: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest
203: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
203: Test timeout computed to be: 1500
70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*]
70: [06:34:59]
70:
70: ****
70: Post-condition Violation
70: Element 'Mv' not found
70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h
70: Failed Expression: anum > -1
70: ----------
70: Stacktrace:
70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 3# 0x00007F82450C8511 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 4# 0x00007F82450D1DEA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 5# 0x00007F82450D216D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1
70: 9# 0x0000563A13E9DCB5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 10# 0x0000563A13F04492 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 11# 0x0000563A13E84A33 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 12# 0x00007F8244633CA8 in /lib/x86_64-linux-gnu/libc.so.6
70: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
70: 14# 0x0000563A13E84B61 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: ----------
70: ****
70:
29: All 191 tests passed
162/235 Test #200: pyTestPropertyLists .................... Passed 0.53 sec
test 204
Start 204: molValidateTest
204: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest
204: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
204: Test timeout computed to be: 1500
163/235 Test #199: pyTestMultithreadedMolSupplier ......... Passed 0.74 sec
test 205
Start 205: molChargeTest
205: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest
205: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
205: Test timeout computed to be: 1500
203: [06:34:59] Can't kekulize mol. Unkekulized atoms: 3 7 8 9
160: file testFlexiCanvas.2a.png gave hash 2907977766U not the expected 2609920321U
160: file testFlexiCanvas.2b.png gave hash 1585391483U not the expected 3615599154U
160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U
188: ....................
188: ----------------------------------------------------------------------
188: Ran 20 tests in 1.410s
188:
188: OK
164/235 Test #205: molChargeTest .......................... Passed 0.10 sec
test 206
Start 206: molTautomerTest
206: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest
206: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
206: Test timeout computed to be: 1500
203: [06:34:59] Initializing Normalizer
203: [06:34:59] Running Normalizer
203: [06:34:59] Rule applied: BrokenazidetoN=N+=N-
203: [06:34:59] Initializing Normalizer
203: [06:34:59] Running Normalizer
203: [06:34:59] Initializing Normalizer
203: [06:34:59] Running Normalizer
201: .
201: ----------------------------------------------------------------------
201: Ran 1 test in 0.012s
201:
201: OK
165/235 Test #203: molNormalizeTest ....................... Passed 0.21 sec
test 207
Start 207: molStandardizeSmallTest
207: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest
207: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
207: Test timeout computed to be: 1500
143: [06:34:59] done
143: [06:34:59] -------------------------------------
143: [06:34:59] Testing GitHubIssue62.
160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U
160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U
160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U
204: ERROR: [FeaturesValidation] Query atom 0 is not allowed
204: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed
204: ERROR: [FeaturesValidation] Query bond 0 is not allowed
204: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed
204: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed
204: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed
204: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed
204: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed
204: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed
204: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed
204: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed
204: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed
204: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed
204: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds.
204: here
204: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order.
204: there
204: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents.
143: [06:34:59] beta-lactam 39.6387
143: [06:34:59] cyclopropanone 174.698
143: [06:34:59] aziridine 337.986
143: [06:34:59] aziridinone 115.248
160: file testGithub4764.sz1.png gave hash 1417438968U not the expected 2179222277U
143: [06:34:59] isobutene 2.48217
143: [06:34:59] acetone 1.91788
169: .........
169: ----------------------------------------------------------------------
169: Ran 9 tests in 2.719s
169:
169: OK
143: [06:34:59] cyclopentanone 10.1648
166/235 Test #204: molValidateTest ........................ Passed 0.24 sec
test 208
Start 208: molFragmentTest
208: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest
208: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
208: Test timeout computed to be: 1500
143: [06:34:59] cyclopropene 99.4921
143: [06:34:59] cyclobutene 41.0156
143: [06:34:59] cyclopropane 267.236
160: file testGithub4764.sz2.png gave hash 2455997703U not the expected 444262090U
143: [06:34:59] gamma-lactam 15.7471
167/235 Test #188: pyRGroupDecomposition .................. Passed 1.94 sec
test 209
Start 209: molStandardizeCatchTest
209: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest
209: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
209: Test timeout computed to be: 1500
168/235 Test #201: pyCDXMLTest ............................ Passed 0.51 sec
test 210
Start 210: molStandardizePipelineTest
210: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest
210: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize
210: Test timeout computed to be: 1500
143: [06:34:59] trans-2,3-diphenylcyclopropan-1-one 203.398
29:
29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf...
169/235 Test #207: molStandardizeSmallTest ................ Passed 0.10 sec
test 211
Start 211: pyMolStandardize
211: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py"
211: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap
211: Test timeout computed to be: 1500
141: [06:34:59] done
141: [06:34:59] -------------------------------------
141: [06:34:59] Testing github 162: Incorrect SMILES after MMFF parameterization .
141: [06:34:59] done
141: [06:34:59] -------------------------------------
141: [06:34:59] Testing github 224: crash during MMFF parameterization .
141: [06:34:59] done
141: [06:34:59] -------------------------------------
141: [06:34:59] Testing github6728: crash due to missing stretch-bend params.
170/235 Test #169: pyMMPA ................................. Passed 3.16 sec
test 212
Start 212: testScaffoldNetwork
212: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork
212: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork
212: Test timeout computed to be: 1500
160: file testGithub4764.sz3.png gave hash 182513311U not the expected 3567162200U
196: .[06:34:59]
196:
196: ****
171/235 Test #141: testMMFFForceFieldHelpers .............. Passed 3.87 sec
148: [06:34:59] Molecule does not have explicit Hs. Consider calling AddHs()
test 213
Start 213: pyScaffoldNetwork
213: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py"
213: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap
213: Test timeout computed to be: 1500
70: [06:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
70: [06:34:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D.
196: Range Error
196: snapshotNum
196: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: 0 < 0
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDKit::Snapshot* (*)(RDKit::Trajectory*, unsigned int), boost::python::return_value_policy<boost::python::manage_new_object, boost::python::default_call_policies>, boost::mpl::vector3<RDKit::Snapshot*, RDKit::Trajectory*, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 21# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 23# _PyObject_MakeTpCall in /usr/bin/python3
196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 25# 0x00000000005BEE79 in /usr/bin/python3
196: 26# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 27# 0x0000000000547080 in /usr/bin/python3
196: 28# 0x00000000006AB720 in /usr/bin/python3
196: 29# _PyObject_MakeTpCall in /usr/bin/python3
196: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 31# 0x00000000005BEE79 in /usr/bin/python3
196: 32# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 33# 0x0000000000547080 in /usr/bin/python3
196: 34# 0x00000000006AB720 in /usr/bin/python3
196: 35# _PyObject_MakeTpCall in /usr/bin/python3
196: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 37# 0x00000000005BEE79 in /usr/bin/python3
196: 38# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 39# 0x0000000000547080 in /usr/bin/python3
196: 40# 0x00000000006AB720 in /usr/bin/python3
196: 41# _PyObject_MakeTpCall in /usr/bin/python3
196: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 43# 0x000000000059582E in /usr/bin/python3
196: 44# _PyObject_MakeTpCall in /usr/bin/python3
196: 45# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 46# PyEval_EvalCode in /usr/bin/python3
196: 47# 0x000000000066A861 in /usr/bin/python3
196: 48# 0x000000000066670C in /usr/bin/python3
196: 49# 0x000000000067F713 in /usr/bin/python3
196: 50# 0x000000000067ECE3 in /usr/bin/python3
196: 51# 0x000000000067EB1E in /usr/bin/python3
196: 52# Py_RunMain in /usr/bin/python3
196: 53# Py_BytesMain in /usr/bin/python3
196: 54# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 56# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: .[06:34:59]
196:
196: ****
196: Pre-condition Violation
196: The trajectory must have dimension == 3
196: Violation occurred on line 113 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: traj.dimension() == 3
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<unsigned int (*)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3<unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: ..[06:34:59]
196:
196: ****
143: [06:34:59] cis-2,3-diphenylcyclopropan-1-one 206.852
196: Pre-condition Violation
196: The trajectory must have dimension == 3
196: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: traj.dimension() == 3
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<unsigned int (*)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3<unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: .[06:34:59]
196:
196: ****
196: Pre-condition Violation
196: d_pos must not be NULL
196: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: d_pos
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDGeom::Point2D (RDKit::Snapshot::*)(unsigned int) const, boost::python::default_call_policies, boost::mpl::vector3<RDGeom::Point2D, RDKit::Snapshot&, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: [06:34:59]
196:
196: ****
196: Pre-condition Violation
196: d_trajectory must not be NULL
196: Violation occurred on line 24 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: d_trajectory
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDGeom::Point2D (RDKit::Snapshot::*)(unsigned int) const, boost::python::default_call_policies, boost::mpl::vector3<RDGeom::Point2D, RDKit::Snapshot&, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: .[06:34:59]
196:
196: ****
210: Randomness seeded to: 764839792
210: 1 Counts line too short: '' on line4
210: 1 Could not instantiate a valid molecule from input
196: Range Error
196: snapshotNum
196: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: 5 < 5
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDKit::Snapshot* (*)(RDKit::Trajectory*, unsigned int), boost::python::return_value_policy<boost::python::manage_new_object, boost::python::default_call_policies>, boost::mpl::vector3<RDKit::Snapshot*, RDKit::Trajectory*, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 21# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 23# _PyObject_MakeTpCall in /usr/bin/python3
196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 25# 0x00000000005BEE79 in /usr/bin/python3
196: 26# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 27# 0x0000000000547080 in /usr/bin/python3
196: 28# 0x00000000006AB720 in /usr/bin/python3
196: 29# _PyObject_MakeTpCall in /usr/bin/python3
196: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 31# 0x00000000005BEE79 in /usr/bin/python3
196: 32# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 33# 0x0000000000547080 in /usr/bin/python3
196: 34# 0x00000000006AB720 in /usr/bin/python3
196: 35# _PyObject_MakeTpCall in /usr/bin/python3
196: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 37# 0x00000000005BEE79 in /usr/bin/python3
196: 38# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 39# 0x0000000000547080 in /usr/bin/python3
196: 40# 0x00000000006AB720 in /usr/bin/python3
196: 41# _PyObject_MakeTpCall in /usr/bin/python3
196: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 43# 0x000000000059582E in /usr/bin/python3
196: 44# _PyObject_MakeTpCall in /usr/bin/python3
196: 45# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 46# PyEval_EvalCode in /usr/bin/python3
196: 47# 0x000000000066A861 in /usr/bin/python3
196: 48# 0x000000000066670C in /usr/bin/python3
196: 49# 0x000000000067F713 in /usr/bin/python3
196: 50# 0x000000000067ECE3 in /usr/bin/python3
196: 51# 0x000000000067EB1E in /usr/bin/python3
196: 52# Py_RunMain in /usr/bin/python3
196: 53# Py_BytesMain in /usr/bin/python3
196: 54# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 56# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: [06:34:59]
196:
196: ****
196: Range Error
196: pointNum
196: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: 10 < 10
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDGeom::Point2D (RDKit::Snapshot::*)(unsigned int) const, boost::python::default_call_policies, boost::mpl::vector3<RDGeom::Point2D, RDKit::Snapshot&, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: .[06:34:59]
196:
196: ****
143: [06:34:59] 2,3-diphenylcyclopropa-2-en-1-one 20.0443
196: Range Error
196: snapshotNum
196: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: 5 < 5
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Trajectory::getSnapshot(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDKit::Snapshot* (*)(RDKit::Trajectory*, unsigned int), boost::python::return_value_policy<boost::python::manage_new_object, boost::python::default_call_policies>, boost::mpl::vector3<RDKit::Snapshot*, RDKit::Trajectory*, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 21# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 23# _PyObject_MakeTpCall in /usr/bin/python3
196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 25# 0x00000000005BEE79 in /usr/bin/python3
196: 26# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 27# 0x0000000000547080 in /usr/bin/python3
196: 28# 0x00000000006AB720 in /usr/bin/python3
196: 29# _PyObject_MakeTpCall in /usr/bin/python3
196: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 31# 0x00000000005BEE79 in /usr/bin/python3
196: 32# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 33# 0x0000000000547080 in /usr/bin/python3
196: 34# 0x00000000006AB720 in /usr/bin/python3
196: 35# _PyObject_MakeTpCall in /usr/bin/python3
196: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 37# 0x00000000005BEE79 in /usr/bin/python3
196: 38# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 39# 0x0000000000547080 in /usr/bin/python3
196: 40# 0x00000000006AB720 in /usr/bin/python3
196: 41# _PyObject_MakeTpCall in /usr/bin/python3
196: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 43# 0x000000000059582E in /usr/bin/python3
196: 44# _PyObject_MakeTpCall in /usr/bin/python3
196: 45# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 46# PyEval_EvalCode in /usr/bin/python3
196: 47# 0x000000000066A861 in /usr/bin/python3
196: 48# 0x000000000066670C in /usr/bin/python3
196: 49# 0x000000000067F713 in /usr/bin/python3
196: 50# 0x000000000067ECE3 in /usr/bin/python3
196: 51# 0x000000000067EB1E in /usr/bin/python3
196: 52# Py_RunMain in /usr/bin/python3
196: 53# Py_BytesMain in /usr/bin/python3
196: 54# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 56# _start in /usr/bin/python3
196: ----------
196: ****
196:
196: [06:34:59]
196:
196: ****
196: Pre-condition Violation
196: d_dimension must be == 2
196: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: d_trajectory->dimension() == 2
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDGeom::Point2D (RDKit::Snapshot::*)(unsigned int) const, boost::python::default_call_policies, boost::mpl::vector3<RDGeom::Point2D, RDKit::Snapshot&, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
143: [06:34:59] cyclopropylidencyclobutane 218.879
196: [06:34:59]
196:
196: ****
196: Pre-condition Violation
196: d_dimension must be == 2
196: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp
196: Failed Expression: d_trajectory->dimension() == 2
196: ----------
196: Stacktrace:
196: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1
196: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDGeom::Point2D (RDKit::Snapshot::*)(unsigned int) const, boost::python::default_call_policies, boost::mpl::vector3<RDGeom::Point2D, RDKit::Snapshot&, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so
196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 5# 0x00007FEB83F2C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
196: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
196: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 11# 0x00007FEB81BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 12# 0x00007FEB81BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 13# 0x00007FEB81BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 14# 0x00007FEB81BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 15# 0x00007FEB81BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
196: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
196: 20# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 21# 0x00007FEB83F293C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
196: 22# _PyObject_MakeTpCall in /usr/bin/python3
196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 24# 0x00000000005BEE79 in /usr/bin/python3
196: 25# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 26# 0x0000000000547080 in /usr/bin/python3
196: 27# 0x00000000006AB720 in /usr/bin/python3
196: 28# _PyObject_MakeTpCall in /usr/bin/python3
196: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 30# 0x00000000005BEE79 in /usr/bin/python3
196: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 32# 0x0000000000547080 in /usr/bin/python3
196: 33# 0x00000000006AB720 in /usr/bin/python3
196: 34# _PyObject_MakeTpCall in /usr/bin/python3
196: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 36# 0x00000000005BEE79 in /usr/bin/python3
196: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 38# 0x0000000000547080 in /usr/bin/python3
196: 39# 0x00000000006AB720 in /usr/bin/python3
196: 40# _PyObject_MakeTpCall in /usr/bin/python3
196: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 42# 0x000000000059582E in /usr/bin/python3
196: 43# _PyObject_MakeTpCall in /usr/bin/python3
196: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
196: 45# PyEval_EvalCode in /usr/bin/python3
196: 46# 0x000000000066A861 in /usr/bin/python3
196: 47# 0x000000000066670C in /usr/bin/python3
196: 48# 0x000000000067F713 in /usr/bin/python3
196: 49# 0x000000000067ECE3 in /usr/bin/python3
196: 50# 0x000000000067EB1E in /usr/bin/python3
196: 51# Py_RunMain in /usr/bin/python3
196: 52# Py_BytesMain in /usr/bin/python3
196: 53# 0x00007FEB846D5CA8 in /lib/x86_64-linux-gnu/libc.so.6
196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
196: 55# _start in /usr/bin/python3
196: ----------
196: ****
196:
160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U
196: .
196: ----------------------------------------------------------------------
196: Ran 9 tests in 0.653s
196:
196: OK
196: Testing Trajectory wrapper
210: 8 Molecule has no atoms
210: [06:34:59] Explicit valence for atom # 1 N, 4, is greater than permitted
210: [06:34:59] Explicit valence for atom # 1 N, 4, is greater than permitted
160: file github5383_2.svg gave hash 2560846108U not the expected 0U
210: 8 Explicit valence for atom # 1 N, 4, is greater than permitted
210: 128 An error occurred while preparing the molecule for standardization.
210: 8 The molecule contains an unknown isotope: 3C
210: 4 Query atom 0 is not allowed
160: file github5383_1.png gave hash 53778753U not the expected 2893520928U
210: 4 Bond 0 of aromatic type is not allowed
210: 4 Bond 1 of aromatic type is not allowed
210: 4 Bond 2 of aromatic type is not allowed
210: 4 Bond 3 of aromatic type is not allowed
210: 4 Bond 5 of aromatic type is not allowed
210: 4 Bond 6 of aromatic type is not allowed
160: file acs1996_1.png gave hash 1997633690U not the expected 2329725800U
210: 4 Bond 2 of dative type is not allowed
210: 4 Bond 3 of dative type is not allowed
143: [06:34:59] diphenylmethylidencyclobutane 79.6139
143: [06:34:59] done
143: [06:34:59] -------------------------------------
143: [06:34:59] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides.
143: [06:34:59] done
143: [06:34:59] -------------------------------------
143: [06:34:59] Test square planar complexes
143: [06:34:59] done
143: [06:34:59] -------------------------------------
143: [06:34:59] Test octahedral complexes
143: [06:34:59] done
210: 4 Enhanced stereochemistry features are not allowed
208: [06:34:59] SMARTS Parse Error: syntax error while parsing: [Cl
208: [06:34:59] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl'
160: file acs1996_2.png gave hash 3378065352U not the expected 2996350718U
160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U
210: 8 The radical at atom 0 is not allowed
172/235 Test #143: testUFFForceFieldHelpers ............... Passed 3.92 sec
test 214
Start 214: pyScaffoldNetworkPickling
214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py"
214: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap
214: Test timeout computed to be: 1500
210: [06:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
173/235 Test #208: molFragmentTest ........................ Passed 0.14 sec
test 215
Start 215: testMolEnumerator
215: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator
215: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator
215: Test timeout computed to be: 1500
210: 16 The molecule includes non-null Z coordinates
210: 32 Atom 0 too close to bond 2
70: ----------------------------------
70: ----------------------------------
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test Issue252: Bad definitions for Crippen atom types.
70: [06:34:59]
70:
70: ****
210: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit
70: Pre-condition Violation
70: rlabel out of range for MDL files
70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp
70: Failed Expression: rlabel >= 0 && rlabel < 100
70: ----------
70: Stacktrace:
70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
70: 3# 0x0000563A13EAB09F in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 4# 0x0000563A13F0450A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 5# 0x0000563A13E84A33 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: 6# 0x00007F8244633CA8 in /lib/x86_64-linux-gnu/libc.so.6
70: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
70: 8# 0x0000563A13E84B61 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1
70: ----------
174/235 Test #196: pyTestTrajectory ....................... Passed 1.43 sec
test 216
Start 216: pyMolEnumerator
216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rough_test.py"
216: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap
216: Test timeout computed to be: 1500
70: ****
70:
70: [06:34:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test calculation of ChiVs.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test calculation of ChiNs.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test calculation of HallKierAlpha.
210: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds
210: 64 Atom 0 has adjacent stereo bonds with like orientation
210: [06:34:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
160: [06:34:59] 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.
210: 16 The molecule includes non-null Z coordinates
210: 64 Atom 0 has adjacent stereo bonds with like orientation
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test calculation of Kappa1.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test calculation of Kappa2.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test calculation of Kappa3.
210: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit
210: 8388608 One or more metal atoms were disconnected.
210: 33554432 One or more disconnected fragments (e.g., counterions) were removed.
210: 67108864 The protonation state was adjusted.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test Crippen atom type calculations.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test ring descriptors
160: file bond_highlights_8.svg gave hash 3610726614U not the expected 3119784980U
210: 16777216 The representation of some functional groups was adjusted.
210: 67108864 The protonation state was adjusted.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test other count descriptors.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test MQN
210: 16777216 The representation of some functional groups was adjusted.
210: 67108864 The protonation state was adjusted.
210: 16777216 The representation of some functional groups was adjusted.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test GitHub Issue 56.
111: [06:34:59] WARNING: not removing hydrogen atom without neighbors
111: [06:34:59] WARNING: not removing hydrogen atom without neighbors
111: [06:34:59] WARNING: not removing hydrogen atom without neighbors
111: [06:34:59] WARNING: not removing hydrogen atom without neighbors
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test Github92: Bad Crippen atom type for pyrrole H.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test Github362: order dependence in Kier-Hall descriptors.
210: 16777216 The representation of some functional groups was adjusted.
210: 67108864 The protonation state was adjusted.
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test calculation of spiro and bridgehead counts.
148: [06:34:59] Molecule does not have explicit Hs. Consider calling AddHs()
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test Github694: ExactMolWt ignoring the mass of the electron
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Testing Properties and KitchenSink
210: 16777216 The representation of some functional groups was adjusted.
210: 67108864 The protonation state was adjusted.
210: 16777216 The representation of some functional groups was adjusted.
210: 67108864 The protonation state was adjusted.
210: 16777216 The representation of some functional groups was adjusted.
210: 67108864 The protonation state was adjusted.
111: [06:34:59] ---Caught keyerror (bad property name)---
111: [06:34:59] -------------------------------------
111: [06:34:59] Test USR Descriptor
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test Github #1973: support P and S terms for TPSA calculation
111: [06:34:59] done
111: [06:34:59] -------------------------------------
111: [06:34:59] Test Github #2948: Empty molecule has non-zero LabuteASA
111: [06:34:59] done
210: 8388608 One or more metal atoms were disconnected.
210: 33554432 One or more disconnected fragments (e.g., counterions) were removed.
210: 67108864 The protonation state was adjusted.
175/235 Test #111: testDescriptors ........................ Passed 4.61 sec
test 217
Start 217: testAbbreviations
217: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations
217: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations
217: Test timeout computed to be: 1500
210: 8388608 One or more metal atoms were disconnected.
210: 33554432 One or more disconnected fragments (e.g., counterions) were removed.
210: 67108864 The protonation state was adjusted.
210: 8388608 One or more metal atoms were disconnected.
210: 33554432 One or more disconnected fragments (e.g., counterions) were removed.
210: 67108864 The protonation state was adjusted.
210: 8388608 One or more metal atoms were disconnected.
210: 33554432 One or more disconnected fragments (e.g., counterions) were removed.
210: 67108864 The protonation state was adjusted.
210: 8388608 One or more metal atoms were disconnected.
210: 33554432 One or more disconnected fragments (e.g., counterions) were removed.
210: 67108864 The protonation state was adjusted.
210: 16777216 The "wavy" style of bond 4 was removed
210: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration
210: 16777216 The "wavy" style of bond 2 was removed
215: Randomness seeded to: 3679440723
215: [06:34:59] can only enumerate SRUs with CONNECT=HT or CONNECT=HH
210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration
210: 16777216 The "wavy" style of bond 1 was removed
194: ............................[06:34:59] unable to set wavy bonds for double bonds: 3
210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration
210: 16777216 The "wavy" style of bond 1 was removed
210: 16777216 The "wavy" style of bond 4 was removed
210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration
210: 16777216 The "wavy" style of bond 3 was removed
217: Randomness seeded to: 692239992
217: [06:34:59] SMARTS Parse Error: syntax error while parsing: *fail
217: [06:34:59] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail'
160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U
210: 16777216 The representation of some functional groups was adjusted.
217: [06:34:59] no suitable SubstanceGroups found
217: ===============================================================================
217: All tests passed (195 assertions in 12 test cases)
217:
176/235 Test #217: testAbbreviations ...................... Passed 0.07 sec
210: [06:34:59] Can't kekulize mol. Unkekulized atoms: 2 3 5
test 218
Start 218: pyAbbreviations
218: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py"
218: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap
218: Test timeout computed to be: 1500
194: .............[06:34:59]
194:
194: ****
194: Range Error
194: idx
194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp
194: Failed Expression: 6 < 5
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 4# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<void (RDKit::ReadWriteMol::*)(unsigned int), boost::python::default_call_policies, boost::mpl::vector3<void, RDKit::ReadWriteMol&, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 26# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 28# _PyObject_MakeTpCall in /usr/bin/python3
194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 30# 0x00000000005BEE79 in /usr/bin/python3
194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 32# 0x0000000000547080 in /usr/bin/python3
194: 33# 0x00000000006AB720 in /usr/bin/python3
194: 34# _PyObject_MakeTpCall in /usr/bin/python3
194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 36# 0x00000000005BEE79 in /usr/bin/python3
194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 38# 0x0000000000547080 in /usr/bin/python3
194: 39# 0x00000000006AB720 in /usr/bin/python3
194: 40# _PyObject_MakeTpCall in /usr/bin/python3
194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 42# 0x00000000005BEE79 in /usr/bin/python3
194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 44# 0x0000000000547080 in /usr/bin/python3
194: 45# 0x00000000006AB720 in /usr/bin/python3
194: 46# _PyObject_MakeTpCall in /usr/bin/python3
194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 48# 0x000000000059582E in /usr/bin/python3
194: 49# _PyObject_MakeTpCall in /usr/bin/python3
194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 51# PyEval_EvalCode in /usr/bin/python3
194: 52# 0x000000000066A861 in /usr/bin/python3
194: 53# 0x000000000066670C in /usr/bin/python3
194: 54# 0x000000000067F713 in /usr/bin/python3
194: 55# 0x000000000067ECE3 in /usr/bin/python3
194: 56# 0x000000000067EB1E in /usr/bin/python3
194: 57# Py_RunMain in /usr/bin/python3
194: 58# Py_BytesMain in /usr/bin/python3
194: 59# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 61# _start in /usr/bin/python3
194: ----------
194: ****
194:
215: ===============================================================================
215: All tests passed (321 assertions in 16 test cases)
215:
210: ===============================================================================
210: All tests passed (268 assertions in 5 test cases)
210:
177/235 Test #215: testMolEnumerator ...................... Passed 0.17 sec
test 219
Start 219: generalizedSubstructCatch
219: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch
219: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct
219: Test timeout computed to be: 1500
178/235 Test #210: molStandardizePipelineTest ............. Passed 0.28 sec
test 220
Start 220: pyGeneralizedSubstruct
220: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py"
220: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap
220: Test timeout computed to be: 1500
12: ..................
12: ----------------------------------------------------------------------
12: Ran 18 tests in 4.929s
12:
12: OK
148: [06:34:59] Molecule does not have explicit Hs. Consider calling AddHs()
70: [06:35:00] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas
70: [06:35:00] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas'
179/235 Test #12: pyBV ................................... Passed 5.20 sec
test 221
Start 221: testMolProcessing
221: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing
221: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing
221: Test timeout computed to be: 1500
214: .
214: ----------------------------------------------------------------------
214: Ran 1 test in 0.020s
214:
214: OK
216: ...
216: ----------------------------------------------------------------------
216: Ran 3 tests in 0.017s
216:
216: OK
70: [06:35:00] Empty atom list: 'M ALS 1 0 F' on line 8.
180/235 Test #70: fileParsersTest1 ....................... Passed 5.06 sec
test 222
Start 222: pyMolProcessing
222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py"
222: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap
222: Test timeout computed to be: 1500
181/235 Test #216: pyMolEnumerator ........................ Passed 0.35 sec
test 223
Start 223: testMIF
223: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF
223: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields
223: Test timeout computed to be: 1500
182/235 Test #214: pyScaffoldNetworkPickling .............. Passed 0.39 sec
test 224
Start 224: pyMIF
224: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py"
224: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap
224: Test timeout computed to be: 1500
213: .......
213: ----------------------------------------------------------------------
213: Ran 7 tests in 0.051s
213:
213: OK
148: [06:35:00] Molecule does not have explicit Hs. Consider calling AddHs()
223: Randomness seeded to: 4207716908
223: ===============================================================================
223: All tests passed (27926 assertions in 8 test cases)
223:
183/235 Test #223: testMIF ................................ Passed 0.09 sec
test 225
Start 225: testQuery
225: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query/testQuery
225: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query
225: Test timeout computed to be: 1500
184/235 Test #213: pyScaffoldNetwork ...................... Passed 0.54 sec
test 226
Start 226: testBaseFeatures
226: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Features/testBaseFeatures
226: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Features
226: Test timeout computed to be: 1500
225: Query
225: Query2
225: Equality
225: Greater
225: GreaterEqual
225: Less
225: LessEqual
225: Open Range
225: Closed Range
225: Float
225: With Tolerance
225: Set
225: And
225: Or
225: XOr
225: pointer and copy foo
225: Set2
160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U
185/235 Test #225: testQuery .............................. Passed 0.01 sec
226: -------------------------------------
226: Basics for ExplicitFeatures.
226: done
226: -------------------------------------
226: Basics for ImplicitFeatures.
226: done
226: -------------------------------------
226: ExplicitFeatures 2D, string type.
226: done
test 227
Start 227: testMatCalc
227: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc
227: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc
227: Test timeout computed to be: 1500
186/235 Test #226: testBaseFeatures ....................... Passed 0.01 sec
test 228
Start 228: pyMatCalc
228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py"
228: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap
228: Test timeout computed to be: 1500
227: 1.68022e+08
227: 1.73149e+08
227: 1.05549e+08
227: 7.20603e+07
227: 1.41535e+08
227: 1.08592e+08
227: 1.11334e+08
227: 2.05553e+08
227: 1.54962e+08
227: 8.08231e+07
227: 5.61421e+07
227: 1.28874e+08
227: 1.59011e+08
227: 8.69902e+07
227: 1.31367e+08
227: 2.27389e+08
227: 1.60289e+08
227: 7.79813e+07
227: 1.61001e+08
227: 2.07599e+08
227: 2.24432e+08
227: 1.39725e+08
227: 2.42614e+08
227: 1.77578e+08
227: 1.05908e+08
227: 9.06742e+07
227: 1.8087e+08
227: 1.98182e+08
227: 2.03052e+08
227: 1.7673e+08
227: 9.32798e+07
227: 1.37969e+08
227: 1.83778e+08
227: 2.1228e+08
227: 5.06157e+07
227: 1.566e+08
227: 2.37142e+08
227: 1.49345e+08
227: 7.05819e+07
227: 1.71633e+08
227: 1.96817e+08
227: 2.18246e+08
227: 9.49496e+07
227: 2.25618e+08
227: 1.30219e+08
187/235 Test #227: testMatCalc ............................ Passed 0.01 sec
test 229
Start 229: testSimDivPickers
229: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers
229: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers
229: Test timeout computed to be: 1500
229: [06:35:00] -------------------------------------
229: [06:35:00] Testing github issue 1421: MaxMinPicker picking non-existent element.
229: [06:35:00] Done
229: [06:35:00] -------------------------------------
229: [06:35:00] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour.
229: [06:35:00] Done
188/235 Test #229: testSimDivPickers ...................... Passed 0.01 sec
test 230
Start 230: pickersTestsCatch
230: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch
230: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers
230: Test timeout computed to be: 1500
218: .......
218: ----------------------------------------------------------------------
218: Ran 7 tests in 0.022s
218:
218: OK
219: Randomness seeded to: 2997988780
219: ===============================================================================
219: All tests passed (486 assertions in 10 test cases)
219:
206: [06:35:00] Tautomer enumeration stopped at 292 tautomers: max transforms reached
189/235 Test #219: generalizedSubstructCatch .............. Passed 0.37 sec
test 231
Start 231: pySimDivPickers
231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/testPickers.py"
231: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap
231: Test timeout computed to be: 1500
190/235 Test #218: pyAbbreviations ........................ Passed 0.39 sec
test 232
Start 232: pyRanker
232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap/testRanker.py"
232: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap
232: Test timeout computed to be: 1500
230: Randomness seeded to: 3369893631
230: ===============================================================================
230: All tests passed (21267 assertions in 1 test case)
230:
191/235 Test #230: pickersTestsCatch ...................... Passed 0.12 sec
test 233
Start 233: testChemicalFeatures
233: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures
233: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures
233: Test timeout computed to be: 1500
163: [06:35:00] The provided InitialSeed is not an MCS and will be ignored
117: =>start test GETAWAY custom
117: [06:35:01] test on : 365 molecules done
192/235 Test #202: molStandardizeTest ..................... Passed 2.53 sec
test 234
Start 234: pyFeatures
234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/testFeatures.py"
234: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap
234: Test timeout computed to be: 1500
193/235 Test #117: testRDFcustom .......................... Passed 6.57 sec
test 235
Start 235: pythonProjectTests
235: Test command: /usr/bin/python3 "-m" "pytest"
235: Working Directory: /build/reproducible-path/rdkit-202409.6/Projects
235: Test timeout computed to be: 1500
150: ***********************************************************
150: Testing O3AAlign
150: ---------------------------------
150: testMMFFO3A
150:
150: ---------------------------------
150: testMMFFO3A with pre-computed dmat and MolHistogram
150:
150: ---------------------------------
150: testMMFFO3A with constraints
150:
150: ---------------------------------
150: testMMFFO3A with variable weight constraints followed by local-only optimization
150:
150: ---------------------------------
150: testCrippenO3A
150:
150: ---------------------------------
150: testCrippenO3A with pre-computed dmat and MolHistogram
150:
150: ---------------------------------
150: testCrippenO3A with constraints
150:
150: ---------------------------------
150: testCrippenO3A with variable weight constraints followed by local-only optimization
150:
150: ---------------------------------
150: testMMFFO3A multithreading
150:
150: generating reference data
233: -----------------------------------------
233: Test1
233: Done
194/235 Test #233: testChemicalFeatures ................... Passed 1.50 sec
148: .[06:35:01] Molecule does not have explicit Hs. Consider calling AddHs()
209: Randomness seeded to: 3099089049
209: * - * - * - * m1
209: * - * - * - * m2
209: * - * - * - * m1
209: * - * - * - * m2
220: .......
220: ----------------------------------------------------------------------
220: Ran 7 tests in 1.723s
220:
220: OK
160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U
209: [06:35:01] Can't kekulize mol. Unkekulized atoms: 3 7
209: [06:35:01] Can't kekulize mol. Unkekulized atoms: 3 8
195/235 Test #220: pyGeneralizedSubstruct ................. Passed 2.06 sec
160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U
209: [06:35:01] Can't kekulize mol. Unkekulized atoms: 2 3 4
160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U
146: validating reference data
160: [06:35:01]
160:
160: ****
160: Pre-condition Violation
160:
160: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp
160: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size()
160: ----------
160: Stacktrace:
160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
160: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector<std::unique_ptr<RDKit::MolDraw2D_detail::DrawShape, std::default_delete<RDKit::MolDraw2D_detail::DrawShape> >, std::allocator<std::unique_ptr<RDKit::MolDraw2D_detail::DrawShape, std::default_delete<RDKit::MolDraw2D_detail::DrawShape> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<int, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> >, std::less<int>, std::allocator<std::pair<int const, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> > > > > const&, std::map<int, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> >, std::less<int>, std::allocator<std::pair<int const, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> > > > > const&, std::map<int, double, std::less<int>, std::allocator<std::pair<int const, double> > > const&, std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 8# 0x000056389D9FEDA5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 9# 0x000056389DAE08C8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 10# 0x000056389DAE13E8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 11# 0x000056389DAE1860 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 12# 0x000056389DAB3403 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 13# 0x000056389DAB376C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 14# 0x000056389D9F75DE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 15# 0x00007F3CFEC33CA8 in /lib/x86_64-linux-gnu/libc.so.6
160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
160: 17# 0x000056389D9F7621 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: ----------
160: ****
160:
160: [06:35:01]
160:
160: ****
160: Range Error
160: idx
160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp
160: Failed Expression: 2 < 0
160: ----------
160: Stacktrace:
160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector<std::unique_ptr<RDKit::MolDraw2D_detail::DrawShape, std::default_delete<RDKit::MolDraw2D_detail::DrawShape> >, std::allocator<std::unique_ptr<RDKit::MolDraw2D_detail::DrawShape, std::default_delete<RDKit::MolDraw2D_detail::DrawShape> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<int, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> >, std::less<int>, std::allocator<std::pair<int const, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> > > > > const&, std::map<int, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> >, std::less<int>, std::allocator<std::pair<int const, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> > > > > const&, std::map<int, double, std::less<int>, std::allocator<std::pair<int const, double> > > const&, std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 8# 0x000056389D9FE512 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 9# 0x000056389DAE08C8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 10# 0x000056389DAE13E8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 11# 0x000056389DAE1860 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 12# 0x000056389DAB3403 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 13# 0x000056389DAB376C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 14# 0x000056389D9F75DE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 15# 0x00007F3CFEC33CA8 in /lib/x86_64-linux-gnu/libc.so.6
160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
160: 17# 0x000056389D9F7621 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: ----------
160: ****
160:
160: [06:35:01]
160:
160: ****
160: Range Error
160: idx
160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp
160: Failed Expression: 0 < 0
160: ----------
160: Stacktrace:
160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector<std::unique_ptr<RDKit::MolDraw2D_detail::DrawShape, std::default_delete<RDKit::MolDraw2D_detail::DrawShape> >, std::allocator<std::unique_ptr<RDKit::MolDraw2D_detail::DrawShape, std::default_delete<RDKit::MolDraw2D_detail::DrawShape> > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<int, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> >, std::less<int>, std::allocator<std::pair<int const, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> > > > > const&, std::map<int, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> >, std::less<int>, std::allocator<std::pair<int const, std::vector<RDKit::DrawColour, std::allocator<RDKit::DrawColour> > > > > const&, std::map<int, double, std::less<int>, std::allocator<std::pair<int const, double> > > const&, std::map<int, int, std::less<int>, std::allocator<std::pair<int const, int> > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1
160: 8# 0x000056389D9FEE78 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 9# 0x000056389DAE08C8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 10# 0x000056389DAE13E8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 11# 0x000056389DAE1860 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 12# 0x000056389DAB3403 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 13# 0x000056389DAB376C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 14# 0x000056389D9F75DE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: 15# 0x00007F3CFEC33CA8 in /lib/x86_64-linux-gnu/libc.so.6
160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
160: 17# 0x000056389D9F7621 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch
160: ----------
160: ****
160:
160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U
231: [06:35:02] the useCache argument is deprecated and ignored
232: ..[06:35:02]
232:
232: ****
232: Invariant Violation
232: Can't rank more bits than the ensemble size
232: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp
232: Failed Expression: num <= dp_maskBits->getNumOnBits()
232: ----------
232: Stacktrace:
232: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
232: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
232: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitInfoTheory.so.1
232: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so
232: 4# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<_object* (*)(RDInfoTheory::InfoBitRanker*, int), boost::python::default_call_policies, boost::mpl::vector3<_object*, RDInfoTheory::InfoBitRanker*, int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so
232: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
232: 6# 0x00007F3034DB862C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
232: 7# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
232: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
232: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
232: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
232: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
232: 12# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
232: 13# 0x00007F3034DB53C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
232: 14# _PyObject_MakeTpCall in /usr/bin/python3
232: 15# _PyEval_EvalFrameDefault in /usr/bin/python3
232: 16# 0x00000000005BEE79 in /usr/bin/python3
232: 17# _PyEval_EvalFrameDefault in /usr/bin/python3
232: 18# 0x0000000000547080 in /usr/bin/python3
232: 19# 0x00000000006AB720 in /usr/bin/python3
232: 20# _PyObject_MakeTpCall in /usr/bin/python3
232: 21# _PyEval_EvalFrameDefault in /usr/bin/python3
232: 22# 0x00000000005BEE79 in /usr/bin/python3
232: 23# _PyEval_EvalFrameDefault in /usr/bin/python3
232: 24# 0x0000000000547080 in /usr/bin/python3
232: 25# 0x00000000006AB720 in /usr/bin/python3
232: 26# _PyObject_MakeTpCall in /usr/bin/python3
232: 27# _PyEval_EvalFrameDefault in /usr/bin/python3
232: 28# 0x00000000005BEE79 in /usr/bin/python3
232: 29# _PyEval_EvalFrameDefault in /usr/bin/python3
232: 30# 0x0000000000547080 in /usr/bin/python3
232: 31# 0x00000000006AB720 in /usr/bin/python3
232: 32# _PyObject_MakeTpCall in /usr/bin/python3
232: 33# _PyEval_EvalFrameDefault in /usr/bin/python3
232: 34# 0x000000000059582E in /usr/bin/python3
232: 35# _PyObject_MakeTpCall in /usr/bin/python3
232: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
232: 37# PyEval_EvalCode in /usr/bin/python3
232: 38# 0x000000000066A861 in /usr/bin/python3
232: 39# 0x000000000066670C in /usr/bin/python3
232: 40# 0x000000000067F713 in /usr/bin/python3
232: 41# 0x000000000067ECE3 in /usr/bin/python3
232: 42# 0x000000000067EB1E in /usr/bin/python3
232: 43# Py_RunMain in /usr/bin/python3
232: 44# Py_BytesMain in /usr/bin/python3
232: 45# 0x00007F303653BCA8 in /lib/x86_64-linux-gnu/libc.so.6
232: 46# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
232: 47# _start in /usr/bin/python3
232: ----------
232: ****
232:
232: ...
232: ----------------------------------------------------------------------
232: Ran 5 tests in 0.023s
232:
232: OK
234: ..
234: ----------------------------------------------------------------------
234: Ran 2 tests in 0.001s
234:
234: OK
234: Testing ChemicalFeatures Wrapper code:
196/235 Test #232: pyRanker ............................... Passed 1.81 sec
197/235 Test #234: pyFeatures ............................. Passed 0.28 sec
206: [06:35:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached
160: ===============================================================================
160: All tests passed (6853 assertions in 115 test cases)
160:
198/235 Test #160: moldraw2DTestCatch ..................... Passed 5.97 sec
231: ...[06:35:02] the useCache argument is deprecated and ignored
231: [06:35:02] the useCache argument is deprecated and ignored
231: .[06:35:02] the useCache argument is deprecated and ignored
206: [06:35:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached
185: iterative
211: .....[06:35:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Test GitHub Issue 258: Bad pattern fingerprint for query molecule
224: .......
224: ----------------------------------------------------------------------
224: Ran 7 tests in 0.106s
224:
224: OK
224: Testing MIF wrapper
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP.
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Test unfolded version of RDKFP
128: [06:35:02] -------------------------------------
128: [06:35:02] Test bitinfo of RDKFP
128: 562: [ 2 ],
128: 709: [ 0 1 ],
128: 1118: [ 0 1 2 ],
128: 1183: [ 1 2 ],
128: 1233: [ 0 1 2 ],
128: 1308: [ 0 ], [ 1 ],
128: 1339: [ 2 ],
128: 1728: [ 1 2 ],
128: 1772: [ 0 ], [ 1 ],
128: 1813: [ 0 1 ],
128: ------------
128: [06:35:02] -------------------------------------
128: [06:35:02] Single atoms setting radius 1 bits in Morgan fingerprints
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Github #879: Pattern fingerprint should set bits for single-atom fragments.
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use AtomPairGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] DEPRECATION WARNING: please use TopologicalTorsionGenerator
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Github #2115: BitInfo not complete for RDKFingerprint
128: [06:35:02] done
128: [06:35:02] -------------------------------------
128: [06:35:02] Github #3723: Fingerprint crash for mols with Zero order bonds
128: [06:35:02] done
199/235 Test #128: testFingerprints ....................... Passed 6.83 sec
200/235 Test #224: pyMIF .................................. Passed 2.30 sec
211: [06:35:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached
228: .....
228: ----------------------------------------------------------------------
228: Ran 5 tests in 0.351s
228:
228: OK
222: ..
222: ----------------------------------------------------------------------
222: Ran 2 tests in 0.222s
222:
222: OK
201/235 Test #228: pyMatCalc .............................. Passed 2.29 sec
206: [06:35:02] Tautomer enumeration stopped at 75 tautomers: canceled
206: Enumeration was canceled due to timeout (50 ms)
212: Randomness seeded to: 855288837
212: ===============================================================================
212: All tests passed (273 assertions in 19 test cases)
212:
202/235 Test #212: testScaffoldNetwork .................... Passed 2.87 sec
203/235 Test #222: pyMolProcessing ........................ Passed 2.46 sec
211: .[06:35:02] Tautomer enumeration stopped at 53 tautomers: canceled
211: Enumeration was canceled due to timeout (50 ms)
194: ....................[06:35:02] Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:02] Explicit valence for atom # 6 F, 2, is greater than permitted
194: [06:35:02] Can't kekulize mol. Unkekulized atoms: 3 4 5
150: processing
150: launch :0
150: launch :1
150: launch :2
150: launch :3
171: Randomness seeded to: 3004406873
171: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/data/chembl_1907596.smi
185: bulk
235: ============================= test session starts ==============================
235: platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0
235: rootdir: /build/reproducible-path/rdkit-202409.6/Projects
235: configfile: pytest.ini
235: collected 12 items
235:
194: .................[06:35:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
206: 375
206: Enumeration has completed
206: [06:35:03] Tautomer enumeration stopped at 73 tautomers: canceled
125: Warning: Atom Count for residue GLU5A does not match expected count
125: Warning: Atom Count for residue ASN39A does not match expected count
125: Warning: Atom Count for residue GLU53A does not match expected count
125: Warning: Atom Count for residue ARG64A does not match expected count
125: Warning: Atom Count for residue LYS80A does not match expected count
125: Warning: Atom Count for residue GLU150A does not match expected count
125: Warning: Atom Count for residue ASN157A does not match expected count
126: Warning: Atom Count for residue GLU5A does not match expected count
126: Warning: Atom Count for residue ASN39A does not match expected count
126: Warning: Atom Count for residue GLU53A does not match expected count
126: Warning: Atom Count for residue ARG64A does not match expected count
126: Warning: Atom Count for residue LYS80A does not match expected count
125: ===============================================================================
125: All tests passed (515 assertions in 10 test cases)
125:
126: Warning: Atom Count for residue GLU150A does not match expected count
126: Warning: Atom Count for residue ASN157A does not match expected count
204/235 Test #125: descriptorsTestCatch ................... Passed 7.85 sec
126: .[06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: .[06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: ..[06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: .[06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: ...[06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: [06:35:03] DEPRECATION WARNING: please use MorganGenerator
126: ....[06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: ....[06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: [06:35:03] DEPRECATION WARNING: please use AtomPairGenerator
126: .[06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: ..[06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: .[06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: [06:35:03] DEPRECATION WARNING: please use TopologicalTorsionGenerator
126: ...
126: ----------------------------------------------------------------------
126: Ran 31 tests in 7.535s
126:
126: OK
126: exactmw 78.046950192
126: amw 78.11399999999999
126: lipinskiHBA 0.0
126: lipinskiHBD 0.0
126: NumRotatableBonds 0.0
126: NumHBD 0.0
126: NumHBA 0.0
126: NumHeavyAtoms 6.0
126: NumAtoms 12.0
126: NumHeteroatoms 0.0
126: NumAmideBonds 0.0
126: FractionCSP3 0.0
126: NumRings 1.0
126: NumAromaticRings 1.0
126: NumAliphaticRings 0.0
126: NumSaturatedRings 0.0
126: NumHeterocycles 0.0
126: NumAromaticHeterocycles 0.0
126: NumSaturatedHeterocycles 0.0
126: NumAliphaticHeterocycles 0.0
126: NumSpiroAtoms 0.0
126: NumBridgeheadAtoms 0.0
126: NumAtomStereoCenters 0.0
126: NumUnspecifiedAtomStereoCenters 0.0
126: labuteASA 37.43140311949697
126: tpsa 0.0
126: CrippenClogP 1.6866
126: CrippenMR 26.441999999999993
126: chi0v 3.464101615137755
126: chi1v 2.0000000000000004
126: chi2v 0.6666666666666671
126: chi3v 0.6666666666666671
126: chi4v 0.38490017945975075
126: chi0n 3.464101615137755
126: chi1n 2.0000000000000004
126: chi2n 0.6666666666666671
126: chi3n 0.6666666666666671
126: chi4n 0.38490017945975075
126: hallKierAlpha -0.78
126: kappa1 3.4115708812260532
126: kappa2 1.6057694396735218
126: kappa3 0.5823992601400448
126: Phi 0.9130327103921437
126: CustomNumAtoms 6.0
126: exactmw 78.046950192
126: lipinskiHBA 0.0
205/235 Test #126: pyMolDescriptors ....................... Passed 7.98 sec
231: .......
231: ----------------------------------------------------------------------
231: Ran 11 tests in 1.469s
231:
231: OK
206/235 Test #231: pySimDivPickers ........................ Passed 3.27 sec
146: processing
146: launch :0
146: launch :1
146: launch :2
146: launch :3
206: CN=c1cc[nH]cn1
206: CN=c1ccnc[nH]1
206: CNc1ccncn1
206: res: CNc1ccncn1
206: CN=c1cccc[nH]1
206: CNc1ccccn1
206: res: CNc1ccccn1
211: Enumeration has completed
221: Randomness seeded to: 2308731582
221: ===============================================================================
221: All tests passed (203 assertions in 1 test case)
221:
207/235 Test #221: testMolProcessing ...................... Passed 4.36 sec
211: [06:35:04] Tautomer enumeration stopped at 32 tautomers: canceled
29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log...
182: [06:35:04] -------------------------------------
182: [06:35:04] testing PatternHolder
29: All 191 tests passed
208/235 Test #206: molTautomerTest ........................ Passed 5.09 sec
211: ..........[06:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted
211: [06:35:04] Explicit valence for atom # 1 N, 4, is greater than permitted
211: [06:35:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
211: [06:35:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
29:
29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.smi...
182: [06:35:04] -------------------------------------
182: [06:35:04] testing TautomerPatternHolder
182: [06:35:04] -------------------------------------
182: [06:35:04] testSegFaultInHolder
182: [06:35:04] SMILES Parse Error: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position [06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] [06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: SMILES Parse Error: [06:35:04] SMILES Parse Error: check for mistakes around position syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position [06:35:04] syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] [06:35:04] [06:35:04] [06:35:04] SMILES Parse Error: [06:35:04] ^
182: SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] [06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: SMILES Parse Error: [06:35:04] dsafsdf1:
182: [06:35:04] dsafsdf[06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: 1SMILES:dsafsdf
182: [06:35:04] ^
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf
182: [06:35:04] ^[06:35:04] 1[06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: 1
182: syntax error while parsing: dsafsdf'SMILES Parse Error:
182:
182: SMILES Parse Error:
182: syntax error[06:35:04] SMILES Parse Error:
182: Parse Error: [06:35:04] ^Failed parsing SMILES 'dsafsdf'[06:35:04] :syntax error
182: while parsing: [06:35:04] : while parsing: dsafsdf[06:35:04] Failed parsing SMILES 'dsafsdf'syntax errorSMILES Parse Error: check for mistakes around position for input: ' while parsing: [06:35:04]
182: dsafsdf
182:
182: [06:35:04] [06:35:04] dsafsdfSMILES Parse Error: check for mistakes around position 1
182:
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: 1:
182: dsafsdf
182: for input: 'dsafsdf
182: [06:35:04] dsafsdf^'SMILES Parse Error: check for mistakes around position [06:35:04] 1:SMILES Parse Error: check for mistakes around position '1:
182:
182:
182: :
182: [06:35:04] [06:35:04] dsafsdf[06:35:04]
182: SMILES
182: SMILESSMILES Parse Error: check for mistakes around position Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[06:35:04] dsafsdf[06:35:04] [06:35:04] dsafsdf1[06:35:04] dsafsdf
182: Parse Error: SMILES
182: [06:35:04] [06:35:04] :' Parse Error:
182: Failed parsing SMILES 'dsafsdf'^
182:
182:
182: [06:35:04] ^
182: ^
182: [06:35:04] dsafsdf
182: [06:35:04] [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: dsafsdf' for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf for input: '
182: [06:35:04]
182: [06:35:04] ^dsafsdfdsafsdf^
182:
182: [06:35:04] '^
182:
182: [06:35:04] SMILES[06:35:04] syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1^[06:35:04]
182: :SMILES
182: [06:35:04]
182: Parse Error: [06:35:04] [06:35:04] SMILES Parse Error: Parse Error: SMILES Parse Error: syntax errordsafsdf while parsing:
182: [06:35:04]
182: Failed parsing SMILES 'dsafsdf'[06:35:04] dsafsdfFailed parsing SMILES 'dsafsdf'[06:35:04] SMILES Parse Error: for input: 'dsafsdfSMILES'
182: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: Parse Error: for input: ' for input: 'dsafsdf
182: Failed parsing SMILES 'dsafsdf'dsafsdf for input: ''[06:35:04] dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: ^
182: '
182: '
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'^dsafsdf
182: '
182: [06:35:04]
182: SMILES Parse Error: [06:35:04] [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'syntax error while parsing: SMILESdsafsdf
182: Parse Error: dsafsdf'
182: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[06:35:04] SMILES Parse Error: syntax error
182: while parsing: dsafsdf[06:35:04] SMILES Parse Error: check for mistakes around position 1:
182:
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] dsafsdf
182: [06:35:04] SMILES Parse Error: for input: 'dsafsdf'
182: [06:35:04] ^
182: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax errorSMILES Parse Error: syntax error[06:35:04] [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182:
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: syntax error while parsing: dsafsdfdsafsdf'[06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf while parsing:
182: SMILES Parse Error: check for mistakes around position 1dsafsdf
182:
182: :
182: [06:35:04] dsafsdf
182:
182: [06:35:04] [06:35:04] SMILES Parse Error: check for mistakes around position [06:35:04] [06:35:04] dsafsdf
182: dsafsdfSMILES Parse Error: check for mistakes around position 1^1:
182: :
182: [06:35:04] [06:35:04]
182: ^^[06:35:04]
182: dsafsdf[06:35:04]
182:
182:
182: [06:35:04] dsafsdf[06:35:04]
182: [06:35:04] [06:35:04] SMILESSMILES Parse Error: SMILES[06:35:04] Failed parsing SMILES 'dsafsdf' for input: ' Parse Error: ^
182: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf^
182: dsafsdf'
182: Parse Error: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf''
182:
182: for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position [06:35:04] 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: syntax error while parsing: [06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position SMILESdsafsdfSMILES Parse Error: syntax error while parsing: [06:35:04] dsafsdf
182:
182: 1: Parse Error:
182: [06:35:04] [06:35:04] dsafsdfFailed parsing SMILES 'dsafsdf'
182: [06:35:04] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1[06:35:04] 1:SMILES Parse Error: check for mistakes around position for input: 'SMILES Parse Error: [06:35:04] dsafsdfSMILES Parse Error: check for mistakes around position :dsafsdf1
182: '
182:
182: syntax error while parsing:
182: dsafsdf:
182: [06:35:04]
182: [06:35:04] [06:35:04] 1dsafsdf
182: dsafsdf[06:35:04]
182: ^[06:35:04] ^[06:35:04] :
182:
182: ^dsafsdf
182:
182: [06:35:04] dsafsdf
182: [06:35:04] [06:35:04] ^[06:35:04] [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'
182: for input: '[06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: dsafsdf'
182: ^
182: SMILES Parse Error: [06:35:04] dsafsdf
182: [06:35:04] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf''
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: ^
182:
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] [06:35:04] SMILES Parse Error: [06:35:04] SMILES Parse Error: [06:35:04] [06:35:04] [06:35:04] SMILES Parse Error: SMILES Parse Error: syntax error[06:35:04] SMILES Parse Error: syntax error[06:35:04] [06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] [06:35:04] [06:35:04] SMILES Parse Error: [06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: SMILES Parse Error: [06:35:04] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: syntax error[06:35:04] Failed parsing SMILES 'dsafsdf'[06:35:04] syntax errorSMILES Parse Error: syntax error while parsing: [06:35:04] while parsing: dsafsdf[06:35:04] [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: SMILES Parse Error: [06:35:04] [06:35:04] [06:35:04] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdfsyntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf[06:35:04]
182: [06:35:04] ^
182: syntax error[06:35:04] [06:35:04] SMILES while parsing: while parsing: [06:35:04] SMILES Parse Error: syntax errordsafsdfdsafsdf while parsing: SMILES Parse Error: [06:35:04] syntax error while parsing: SMILES Parse Error: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position SMILES Parse Error: 1syntax errorSMILES Parse Error: SMILES Parse Error: [06:35:04] syntax error while parsing: while parsing:
182: dsafsdf for input: 'SMILES Parse Error: SMILES Parse Error: dsafsdf Parse Error: syntax error while parsing: syntax errordsafsdf while parsing: SMILES Parse Error:
182: syntax error while parsing: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdfsyntax errordsafsdfdsafsdf
182:
182: [06:35:04] while parsing: syntax errordsafsdf
182: SMILES Parse Error: dsafsdfsyntax error while parsing: syntax error[06:35:04] SMILES Parse Error: syntax error while parsing: while parsing:
182: while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position
182: 1:
182: :[06:35:04] dsafsdfdsafsdf
182: [06:35:04] ^
182:
182: [06:35:04]
182:
182: while parsing: dsafsdf[06:35:04] [06:35:04] SMILES Parse Error:
182:
182: [06:35:04] [06:35:04] dsafsdfSMILES Parse Error: check for mistakes around position '1:
182: SMILES Parse Error: check for mistakes around position [06:35:04] dsafsdfsyntax error[06:35:04] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position
182: [06:35:04] while parsing: [06:35:04] [06:35:04]
182: '
182: [06:35:04] 1dsafsdfsyntax error
182: while parsing: dsafsdf
182: [06:35:04] 1SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position [06:35:04] dsafsdf[06:35:04] SMILES Parse Error: check for mistakes around position while parsing: SMILES Parse Error: check for mistakes around position dsafsdf1
182: dsafsdf[06:35:04] 1:[06:35:04]
182:
182: dsafsdf1[06:35:04] dsafsdfdsafsdfSMILES Parse Error: check for mistakes around position SMILES Parse Error: 1[06:35:04] 1:
182: [06:35:04] :
182: [06:35:04]
182: SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] [06:35:04] SMILES Parse Error: SMILES Parse Error: [06:35:04] syntax error
182: :^
182: SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position :
182: 1syntax error[06:35:04] while parsing: ^
182:
182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182:
182: [06:35:04] dsafsdf
182: [06:35:04] ^1[06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182:
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: check for mistakes around position [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: :
182: dsafsdf[06:35:04]
182: ::
182: [06:35:04]
182:
182: :
182: [06:35:04] dsafsdf while parsing:
182: dsafsdf[06:35:04]
182: [06:35:04] [06:35:04] SMILES Parse Error: check for mistakes around position :[06:35:04]
182: '[06:35:04] dsafsdf
182: [06:35:04] syntax error while parsing: dsafsdf
182:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182:
182: [06:35:04] dsafsdf[06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: dsafsdf[06:35:04]
182: dsafsdf
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: dsafsdf
182:
182: [06:35:04] [06:35:04] [06:35:04] dsafsdf
182: SMILES Parse Error: [06:35:04] 1^
182: :
182: [06:35:04] [06:35:04] dsafsdf[06:35:04] [06:35:04]
182: SMILES Parse Error: check for mistakes around position 1:[06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: SMILES Parse Error: check for mistakes around position 1
182: ^Failed parsing SMILES 'dsafsdf'^
182: SMILES[06:35:04] SMILES Parse Error: [06:35:04] syntax error while parsing: dsafsdf
182: SMILES Parse Error: check for mistakes around position :SMILES Parse Error: [06:35:04] syntax error while parsing: dsafsdf^[06:35:04] SMILES Parse Error: check for mistakes around position ^
182: 1[06:35:04] [06:35:04]
182: 1 Parse Error: ^ for input: '
182: :SMILES
182: [06:35:04]
182: dsafsdf[06:35:04] [06:35:04]
182: dsafsdfdsafsdf1 Parse Error: :
182:
182:
182: ^Failed parsing SMILES 'dsafsdf'[06:35:04] [06:35:04] :^SMILES Parse Error: check for mistakes around position [06:35:04] dsafsdf'
182: for input: '[06:35:04] dsafsdf
182: [06:35:04] dsafsdf[06:35:04] 1dsafsdf
182: SMILES Parse Error: check for mistakes around position
182: [06:35:04] dsafsdf[06:35:04]
182:
182: ^[06:35:04] SMILES Parse Error:
182: SMILES Parse Error: :Failed parsing SMILES 'dsafsdf'1
182: :[06:35:04]
182: ^[06:35:04] [06:35:04] 'SMILES Parse Error:
182: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: syntax error while parsing: dsafsdf
182: Failed parsing SMILES 'dsafsdf'
182: [06:35:04]
182: for input: '[06:35:04] dsafsdf[06:35:04] 'SMILES Parse Error: SMILESsyntax error
182: for input: '[06:35:04]
182: dsafsdf[06:35:04] SMILES Parse Error: dsafsdf
182: Parse Error: [06:35:04] Failed parsing SMILES 'dsafsdf'
182: [06:35:04] [06:35:04] dsafsdf'
182: [06:35:04] ^^^
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: for input: '[06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES
182: [06:35:04] ^
182: Failed parsing SMILES 'dsafsdf'SMILES[06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf Parse Error:
182: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: check for mistakes around position for input: '[06:35:04] [06:35:04] SMILES[06:35:04] for input: ' Parse Error: dsafsdfFailed parsing SMILES 'dsafsdf''[06:35:04]
182: SMILES1 Parse Error: :' for input: '^
182: Parse Error: SMILES
182: Failed parsing SMILES 'dsafsdf' for input: '
182: ^
182: dsafsdf[06:35:04] 'Failed parsing SMILES 'dsafsdf'
182: [06:35:04] for input: '
182: dsafsdfSMILES
182: Parse Error: [06:35:04] for input: 'SMILESdsafsdfdsafsdf[06:35:04] Parse Error: SMILES[06:35:04] Parse Error: SMILESdsafsdfFailed parsing SMILES 'dsafsdf''
182: for input: ' while parsing: Failed parsing SMILES 'dsafsdf'dsafsdf for input: 'dsafsdf' Parse Error: [06:35:04] '''[06:35:04]
182:
182: Failed parsing SMILES 'dsafsdf'
182: syntax error
182:
182: SMILES[06:35:04] Parse Error: Failed parsing SMILES 'dsafsdf'
182: dsafsdfSMILES' Parse Error: Failed parsing SMILES 'dsafsdf' Parse Error:
182: SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] SMILES Parse Error: check for mistakes around position [06:35:04] 1:
182: SMILES Parse Error: check for mistakes around position [06:35:04] [06:35:04] dsafsdf
182: Failed parsing SMILES 'dsafsdf' for input: '[06:35:04] ^[06:35:04] dsafsdfdsafsdfdsafsdf[06:35:04] SMILES Parse Error: check for mistakes around position [06:35:04] '^
182:
182: SMILES Parse Error: 1SMILES Parse Error:
182: Failed parsing SMILES 'dsafsdf' for input: ':dsafsdf1[06:35:04]
182: ^
182: [06:35:04] [06:35:04] syntax error[06:35:04] syntax error':dsafsdf
182: [06:35:04] while parsing:
182: SMILES Parse Error: [06:35:04] Failed parsing SMILES 'dsafsdf' while parsing: for input: 'dsafsdfdsafsdfSMILESdsafsdf
182: SMILES Parse Error: check for mistakes around position
182: SMILES[06:35:04] Parse Error: SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf' for input: ''dsafsdf
182: 1 for input: '
182: '[06:35:04]
182: 1dsafsdf
182: ::
182: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf
182: dsafsdf[06:35:04] dsafsdf
182:
182: [06:35:04] [06:35:04] [06:35:04] '^dsafsdf
182: '
182:
182:
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[06:35:04] for input: 'SMILES Parse Error: check for mistakes around position ^1:
182: [06:35:04] ^
182: dsafsdf[06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf''[06:35:04]
182: SMILES
182: Parse Error: Failed parsing SMILES 'dsafsdf' for input: '
182: [06:35:04] for input: 'dsafsdf^'
182:
182: [06:35:04] [06:35:04] SMILES Parse Error: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf'
182: [06:35:04] SMILES Parse Error: for input: 'dsafsdf
182: syntax error while parsing: syntax errordsafsdf while parsing: dsafsdf[06:35:04] dsafsdf
182: '
182: [06:35:04] SMILES[06:35:04] Parse Error: SMILES Parse Error: check for mistakes around position ^1
182: :
182: [06:35:04]
182: SMILES Parse Error: check for mistakes around position 1:Failed parsing SMILES 'dsafsdf' for input: '[06:35:04] dsafsdf
182:
182: [06:35:04] [06:35:04] [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: ^dsafsdfdsafsdf'
182:
182:
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: while parsing: for input: 'SMILES Parse Error: syntax error while parsing: SMILES Parse Error: [06:35:04] syntax error while parsing: [06:35:04] dsafsdf
182: dsafsdfSMILES Parse Error: check for mistakes around position SMILES Parse Error: 1dsafsdf:
182: [06:35:04] dsafsdf
182: 'syntax error while parsing: dsafsdf
182: [06:35:04] [06:35:04] [06:35:04] dsafsdf
182: SMILES Parse Error: check for mistakes around position
182: SMILES Parse Error: check for mistakes around position [06:35:04] 11
182: SMILES Parse Error: check for mistakes around position :[06:35:04] :SMILES Parse Error: check for mistakes around position
182: ^[06:35:04] 11
182:
182: :
182: [06:35:04] [06:35:04] dsafsdfdsafsdfdsafsdf:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182:
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182:
182: [06:35:04] ^
182: [06:35:04] [06:35:04] SMILESSMILES Parse Error: for input: 'dsafsdf
182: Parse Error: Failed parsing SMILES 'dsafsdf'syntax error while parsing: for input: ''dsafsdf'
182:
182: [06:35:04] dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] ^
182: dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '
182: dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf
182: [06:35:04] SMILES Parse Error: check for mistakes around position 1:
182: [06:35:04] dsafsdf
182: [06:35:04] ^
182: [06:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'
182: [06:35:05] -------------------------------------
182: [06:35:05] Results do not depend on numThreads
164: ........................................[06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: [06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: [06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: .[06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: [06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: [06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: .[06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: [06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: [06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: .[06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: [06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: [06:35:05] The provided InitialSeed is not an MCS and will be ignored
164: .................
164: ----------------------------------------------------------------------
164: Ran 60 tests in 8.665s
164:
164: OK
209/235 Test #164: pyFMCS ................................. Passed 9.13 sec
173: [06:35:05] Building the fingerprints may take some time.
75: [06:35:05] Finished: testSmiCorrectness()
75: [06:35:05] -----------------------------------------
75:
75: [06:35:05]
75: -----------------------------------------
75: [06:35:05] Spurious data before the first property will be ignored
75: [06:35:05] Property <ID> will be truncated after the first blank line
75: [06:35:05] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
75: [06:35:05] Property <ID> will be truncated after the first blank line
185: bulk, no symmetry
210/235 Test #198: pyTestThreads .......................... Passed 7.42 sec
75: [06:35:06] Finished: testSDCorrectness()
75: [06:35:06] -----------------------------------------
75:
211/235 Test #75: testMultithreadedMolSupplier ........... Passed 11.01 sec
159: Done
159: ----------------- Test Github #781: Rendering single-atom molecules
159: Done
159: ----------------- Test 3
159: file test3_1.png gave hash 4245589364U not the expected 675908852U
159: file test3_2.png gave hash 3367333300U not the expected 2452584093U
159: file test3_3.png gave hash 2996581333U not the expected 1907006999U
159: file test3_4.png gave hash 3977004105U not the expected 2305641511U
159: file test3_5.png gave hash 3967750587U not the expected 3842605920U
159: file test3_6.png gave hash 691593501U not the expected 662622011U
159: file test3_7.png gave hash 1614455692U not the expected 469729412U
159: Done
159: ----------------- Test Github774: upside-down drawings
159: file test774_1.png gave hash 383494043U not the expected 428322245U
159: file test774_2.png gave hash 2504225659U not the expected 4095288521U
159: Done
159: ----------------- Test 9 (molecule legends)
159: file test9_1.svg gave hash 923579170U not the expected 1484349178U
159: Done
159: ----------------- Test Github852: Lines used to wedge bonds are too thick
159: file test852_1.png gave hash 2064209894U not the expected 271517011U
159: file test852_2.png gave hash 869339719U not the expected 967452082U
159: ----------------
159: ----------------
159: ----------------
159: ----------------
159: Done
159: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right
159: file test860_1.png gave hash 1884717540U not the expected 2835587240U
159: file test860_2.png gave hash 3946798084U not the expected 1116015475U
159: file test860_3.png gave hash 2321130724U not the expected 1872467868U
159: Done
159: ----------------- Test Github #910: ugly coordinates generated for peptide chains
159: Done
159: ----------------- Test Github #932: mistake in SVG for wedged bonds
159: Done
159: ----------------- Test Github #953: default color should not be cyan
159: Done
159: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly
159: Done
159: ----------------- Test Deuterium, Tritium
159: Done
159: ----------------- Test crossed bonds
159: Done
159: ----------------- Testing drawing a second molecule
159: Done
159: ----------------- Testing drawing a grid of molecules
159: Done
159: ----------------- Testing drawMolecules
159: file test12_1.svg gave hash 76786371U not the expected 826649652U
211: ............[06:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
211: [06:35:06] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored.
211: [06:35:06] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored.
159: Done
159: ----------------- Test JSON Configuration
159: Done
159: ----------------- Testing github 1090: escape html characters in SVG output
176: VS001: PASSED
176: VS002: PASSED
176: VS003: PASSED
176: VS004: PASSED
176: VS005: PASSED
176: VS006: PASSED
176: VS007: PASSED
176: VS008: PASSED
176: VS009: PASSED
176: VS010: PASSED
176: VS011: PASSED
176: VS012: PASSED
176: VS013: PASSED
176: VS014: PASSED
176: VS015: PASSED
176: VS016: PASSED
176: VS017: PASSED
176: VS018: PASSED
176: VS019: PASSED
176: VS020: PASSED
176: VS021: PASSED
176: VS022: PASSED
176: VS023: PASSED
176: VS024: PASSED
176: VS025: PASSED
176: VS026: PASSED
176: VS027: PASSED
176: VS028: PASSED
176: VS029: PASSED
176: VS030: PASSED
176: VS031: PASSED
176: VS032: PASSED
176: VS033: PASSED
176: VS034: PASSED
176: VS035: PASSED
176: VS036: PASSED
176: VS037: PASSED
176: VS038: PASSED
176: VS039: PASSED
176: VS040: PASSED
176: VS041: PASSED
176: VS042: PASSED
176: VS043: PASSED
176: VS044: PASSED
176: VS045: PASSED
176: VS046: PASSED
176: VS047: PASSED
176: VS048: PASSED
176: VS049: PASSED
176: VS050: PASSED
176: VS051: PASSED
176: VS052: PASSED
176: VS053: PASSED
176: VS054: PASSED
176: VS055: PASSED
176: VS056: PASSED
176: VS057: PASSED
176: VS058: PASSED
176: VS059: PASSED
176: VS060: PASSED
176: VS061: PASSED
176: VS062: PASSED
176: VS063: PASSED
176: VS064: PASSED
176: VS065: PASSED
176: VS066: PASSED
176: VS067: PASSED
176: VS068: PASSED
176: VS069: PASSED
176: VS070: PASSED
176: VS071: PASSED
176: VS072: PASSED
176: VS073: PASSED
176: VS074: PASSED
176: VS075: PASSED
176: VS076: PASSED
176: VS077: PASSED
176: VS078: PASSED
176: VS079: PASSED
176: VS080: PASSED
176: VS081: PASSED
176: VS082: PASSED
176: VS083: PASSED
176: VS084: PASSED
176: VS085: PASSED
176: VS086: PASSED
176: VS087: PASSED
176: VS088: PASSED
176: VS089: PASSED
176: VS090: PASSED
176: VS091: PASSED
176: VS092: PASSED
176: VS093: PASSED
176: VS094: PASSED
176: VS095: PASSED
176: VS096: PASSED
176: VS097: PASSED
176: VS098: PASSED
176: VS099: PASSED
176: VS100: PASSED
176: VS101: PASSED
176: VS102: PASSED
176: VS103: PASSED
176: VS104: PASSED
176: VS105: PASSED
176: VS106: PASSED
176: VS107: PASSED
176: VS108: PASSED
176: VS109: PASSED
176: VS110: PASSED
176: VS111: PASSED
176: VS112: PASSED
176: VS113: PASSED
176: VS114: PASSED
176: VS115: PASSED
176: VS116: PASSED
176: VS117: PASSED
176: VS118: PASSED
176: VS119: PASSED
176: VS120: PASSED
176: VS121: PASSED
176: VS122: PASSED
176: VS123: PASSED
176: VS124: PASSED
176: VS125: PASSED
176: VS126: PASSED
176: VS127: PASSED
176: VS128: PASSED
176: VS129: PASSED
176: VS130: PASSED
176: VS131: PASSED
176: VS132: PASSED
176: VS133: PASSED
176: VS134: PASSED
176: VS135: PASSED
176: VS136: PASSED
176: VS137: PASSED
176: VS138: PASSED
176: VS139: PASSED
176: VS140: PASSED
176: VS141: PASSED
176: VS142: PASSED
176: VS143: PASSED
176: VS144: PASSED
176: VS145: PASSED
176: VS146: PASSED
176: VS147: PASSED
176: VS148: PASSED
176: VS149: PASSED
176: VS150: PASSED
176: VS151: PASSED
176: VS152: PASSED
176: VS153: PASSED
176: VS154: PASSED
176: VS155: PASSED
176: VS156: PASSED
176: VS157: PASSED
176: VS158: PASSED
176: VS159: PASSED
176: VS160: PASSED
176: VS161: PASSED
176: VS162: PASSED
176: VS163: PASSED
176: VS164: PASSED
176: VS165: PASSED
176: VS166: PASSED
176: VS167: PASSED
176: VS168: PASSED
176: VS169: PASSED
176: VS170: PASSED
176: VS171: PASSED
176: VS172: PASSED
176: VS173: PASSED
176: VS174: PASSED
176: VS175: PASSED
176: VS176: PASSED
176: VS177: PASSED
176: VS178: PASSED
176: VS179: PASSED
176: VS180: PASSED
176: VS181: PASSED
176: VS182: PASSED
176: VS183: PASSED
176: VS184: PASSED
176: VS185: PASSED
176: VS186: PASSED
176: VS187: PASSED
176: VS188: PASSED
176: VS189: PASSED
176: VS190: PASSED
176: VS191: PASSED
176: VS192: PASSED
176: VS193: PASSED
176: VS194: PASSED
176: VS195: PASSED
176: VS196: PASSED
176: VS197: PASSED
176: VS198: PASSED
176: VS199: PASSED
176: VS200: PASSED
176: VS201: PASSED
176: VS202: PASSED
176: VS203: PASSED
176: VS204: PASSED
176: VS205: PASSED
176: VS206: PASSED
176: VS207: PASSED
176: VS208: PASSED
176: VS209: PASSED
176: VS210: PASSED
176: VS211: PASSED
176: VS212: PASSED
176: VS213: PASSED
176: VS214: PASSED
176: VS215: PASSED
176: VS216: PASSED
176: VS217: PASSED
176: VS218: PASSED
176: VS219: PASSED
176: VS220: PASSED
176: VS221: PASSED
176: VS222: PASSED
176: VS223: PASSED
176: VS224: PASSED
176: VS225: PASSED
176: VS226: PASSED
176: VS227: PASSED
176: VS228: PASSED
176: VS229: PASSED
176: VS230: PASSED
176: VS231: PASSED
176: VS232: PASSED
176: VS233: PASSED
176: VS234: PASSED
176: VS235: PASSED
176: VS236: PASSED
176: VS237: PASSED
176: VS238: PASSED
176: VS239: PASSED
176: VS240: PASSED
176: VS241: PASSED
176: VS242: PASSED
176: VS243: PASSED
176: VS244: PASSED
176: VS245: PASSED
176: VS246: PASSED
176: VS247: PASSED
176: VS248: PASSED
176: VS249: PASSED
176: VS250: PASSED
176: VS251: PASSED
176: VS252: PASSED
176: VS253: PASSED
176: VS254: PASSED
176: VS255: PASSED
176: VS256: PASSED
176: VS257: PASSED
176: VS258: PASSED
176: VS259: PASSED
176: VS260: PASSED
176: VS261: PASSED
176: VS262: PASSED
176: VS263: PASSED
176: VS264: PASSED
176: VS265: PASSED
176: VS266: PASSED
176: VS267: PASSED
176: VS268: PASSED
176: VS269: PASSED
176: VS270: PASSED
176: VS271: PASSED
176: VS272: PASSED
176: VS273: PASSED
176: VS274: PASSED
176: VS275: PASSED
176: VS276: PASSED
176: VS277: PASSED
176: VS278: PASSED
176: VS279: PASSED
176: VS280: PASSED
176: VS281: PASSED
176: VS282: PASSED
176: VS283: PASSED
176: VS284: PASSED
176: VS285: PASSED
176: VS286: PASSED
176: VS287: PASSED
176: VS288: PASSED
176: VS289: PASSED
176: VS290: PASSED
176: VS291: PASSED
176: VS292: PASSED
176: VS293: PASSED
176: VS294: PASSED
176: VS295: PASSED
176: VS296: PASSED
176: VS297: PASSED
176: VS298: PASSED
176: VS299: PASSED
176: VS300: PASSED
176: Check finished: 0 molecules failed.
176: Failed:
159: Done
159: ----------------- Testing github 1035: overflow bug in SVG color generation
159: Done
159: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes
159: Done
159: ----------------- Testing github 1322: add custom atom labels
159: Done
159: ----------------- Testing use of a black & white palette
159: Done
159: ----------------- Testing use of continuous highlighting with drawMolecules
159: Done
159: ----------------- Test 17 - Testing maximum font size
159: Done
159: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list
159: Done
159: ----------------- Testing use of fixed scales for drawing.
212/235 Test #176: pyCIPLabelsValidation .................. Passed 9.75 sec
159: Done
159: ----------------- Testing rotation of 2D drawing.
159: Done
159: ----------------- Testing inclusion of molecule metadata
159: Done
159: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default
159: Done
159: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions
159: file testGithub2151_1.svg gave hash 3620378781U not the expected 4119581143U
159: file testGithub2151_2.svg gave hash 3896781930U not the expected 425960913U
159: Done
159: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn
159: Done
159: ----------------- Testing testGithub2931: multi-coloured molecule highlights.
159: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U
159: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U
159: Done
159: ----------------- Testing annotation of 2D Drawing.
159: file test20_1.png gave hash 1526801019U not the expected 200877868U
159: file test20_2.png gave hash 1568015929U not the expected 1651164846U
159: file test20_3.png gave hash 2265759724U not the expected 1463603076U
159: file test20_4.png gave hash 960727959U not the expected 1714613205U
211: ........[06:35:06] Explicit valence for atom # 1 O, 3, is greater than permitted
159: Done
159: ----------------- Test 21 - different font
159: Done
159: ----------------- Test 22 - draw explicit methyls.
159: Done
159: ----------------- Testing drawing of legends.
159: Done
159: ----------------- Test Github 3305 - change and scale line widths.
159: file testGithub3305_1.png gave hash 4250074512U not the expected 3303791649U
159: file testGithub3305_2.png gave hash 2438913291U not the expected 4003267433U
159: file testGithub3305_3.png gave hash 1680056767U not the expected 273338209U
211: ..
211: ----------------------------------------------------------------------
211: Ran 38 tests in 6.728s
211:
211: OK
211: done
159: file testGithub3305_4.png gave hash 3967750587U not the expected 3842605920U
159: file testGithub3305_5.png gave hash 2464937348U not the expected 151279576U
159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U
159: file testGithub3305_6.png gave hash 1984494277U not the expected 613418460U
185: [06:35:06] Relabelling existing label
159: file testGithub3305_7.png gave hash 2361405774U not the expected 2835747678U
213/235 Test #211: pyMolStandardize ....................... Passed 7.16 sec
159: Done
159: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules.
159: Done
159: ----------------- Test Github 4156 - bad scale for radicals in grid
159: Done
159: ----------------- Test JSON atomColourPalette
159: Done
159: ----------------- Test draw aromatic OR queries
159: Done
159: ----------------- Test AND queries
159: Done
214/235 Test #159: moldraw2DTest1 ......................... Passed 10.66 sec
185: Best mapping
215/235 Test #185: testRGroupDecomp ....................... Passed 9.50 sec
170: Randomness seeded to: 4216257397
170: [06:35:07] Timed out after 11 seconds.
182: [06:35:08] -------------------------------------
182: [06:35:08] Results do not depend on numThreads (all same)
182: [06:35:08] -------------------------------------
182: [06:35:08] testTautomerQueries
81: ===============================================================================
81: All tests passed (1601 assertions in 100 test cases)
81:
216/235 Test #81: fileParsersCatchTest ................... Passed 13.02 sec
182: [06:35:08] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring...
182: [06:35:08] -------------------------------------
182: [06:35:08] github3881 recursive smarts with rings
217/235 Test #182: substructLibraryTest ................... Passed 10.93 sec
29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log...
29: All 191 tests passed
29:
29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi...
184: ......[06:35:08]
184:
184: ****
184: Pre-condition Violation
184: RingInfo not initialized
184: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp
184: Failed Expression: df_init
184: ----------
184: Stacktrace:
184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
184: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
184: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1
184: 4# Queries::AndQuery<int, RDKit::Atom const*, true>::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
184: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 6# boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 7# bool boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll<std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(unsigned int*, unsigned int*, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 8# bool boost::vf2_all<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS>, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const&, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 10# bool RDKit::SubstructMatch<RDKit::ROMol const, RDKit::ROMol>(RDKit::ROMol const&, RDKit::ROMol const&, std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 11# bool RDKit::HasSubstructMatch<RDKit::ROMol const, RDKit::ROMol const>(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 12# 0x00007F4177C5B915 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 14# 0x00007F417A02462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 15# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
184: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
184: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
184: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 20# 0x00007F4177BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 21# 0x00007F4177BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 22# 0x00007F4177BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 23# 0x00007F4177BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 24# 0x00007F4177BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 25# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
184: 26# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
184: 27# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
184: 28# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
184: 29# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 30# 0x00007F417A0213C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 31# _PyObject_MakeTpCall in /usr/bin/python3
184: 32# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 33# 0x00000000005BEE79 in /usr/bin/python3
184: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 35# 0x0000000000547080 in /usr/bin/python3
184: 36# 0x00000000006AB720 in /usr/bin/python3
184: 37# _PyObject_MakeTpCall in /usr/bin/python3
184: 38# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 39# 0x00000000005BEE79 in /usr/bin/python3
184: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 41# 0x0000000000547080 in /usr/bin/python3
184: 42# 0x00000000006AB720 in /usr/bin/python3
184: 43# _PyObject_MakeTpCall in /usr/bin/python3
184: 44# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 45# 0x00000000005BEE79 in /usr/bin/python3
184: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 47# 0x0000000000547080 in /usr/bin/python3
184: 48# 0x00000000006AB720 in /usr/bin/python3
184: 49# _PyObject_MakeTpCall in /usr/bin/python3
184: 50# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 51# 0x000000000059582E in /usr/bin/python3
184: 52# _PyObject_MakeTpCall in /usr/bin/python3
184: 53# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 54# PyEval_EvalCode in /usr/bin/python3
184: 55# 0x000000000066A861 in /usr/bin/python3
184: 56# 0x000000000066670C in /usr/bin/python3
184: 57# 0x000000000067F713 in /usr/bin/python3
184: 58# 0x000000000067ECE3 in /usr/bin/python3
184: 59# 0x000000000067EB1E in /usr/bin/python3
184: 60# Py_RunMain in /usr/bin/python3
184: 61# Py_BytesMain in /usr/bin/python3
184: 62# 0x00007F417A967CA8 in /lib/x86_64-linux-gnu/libc.so.6
184: 63# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
184: 64# _start in /usr/bin/python3
184: ----------
184: ****
184:
184: [06:35:08]
184:
184: ****
184: Pre-condition Violation
184: RingInfo not initialized
184: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp
184: Failed Expression: df_init
184: ----------
184: Stacktrace:
184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
184: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
184: 3# 0x00007F41776E6C80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
184: 4# Queries::EqualityQuery<int, RDKit::Bond const*, true>::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
184: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 6# boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 7# bool boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll<std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(unsigned int*, unsigned int*, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 8# bool boost::detail::VF2SubState<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll<std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(unsigned int*, unsigned int*, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 9# bool boost::vf2_all<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS>, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > > >(boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const&, boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, RDKit::Atom*, RDKit::Bond*, boost::no_property, boost::listS> const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >, std::allocator<std::vector<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1
184: 11# bool RDKit::SubstructMatch<RDKit::ROMol const, RDKit::ROMol>(RDKit::ROMol const&, RDKit::ROMol const&, std::vector<std::pair<int, int>, std::allocator<std::pair<int, int> > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 12# bool RDKit::HasSubstructMatch<RDKit::ROMol const, RDKit::ROMol const>(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 13# 0x00007F4177C5B915 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 15# 0x00007F417A02462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 16# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
184: 18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
184: 19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
184: 20# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 21# 0x00007F4177BB69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 22# 0x00007F4177BB6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 23# 0x00007F4177BB6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 24# 0x00007F4177BB6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 25# 0x00007F4177BB6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
184: 26# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
184: 27# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
184: 28# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
184: 29# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
184: 30# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 31# 0x00007F417A0213C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
184: 32# _PyObject_MakeTpCall in /usr/bin/python3
184: 33# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 34# 0x00000000005BEE79 in /usr/bin/python3
184: 35# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 36# 0x0000000000547080 in /usr/bin/python3
184: 37# 0x00000000006AB720 in /usr/bin/python3
184: 38# _PyObject_MakeTpCall in /usr/bin/python3
184: 39# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 40# 0x00000000005BEE79 in /usr/bin/python3
184: 41# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 42# 0x0000000000547080 in /usr/bin/python3
184: 43# 0x00000000006AB720 in /usr/bin/python3
184: 44# _PyObject_MakeTpCall in /usr/bin/python3
184: 45# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 46# 0x00000000005BEE79 in /usr/bin/python3
184: 47# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 48# 0x0000000000547080 in /usr/bin/python3
184: 49# 0x00000000006AB720 in /usr/bin/python3
184: 50# _PyObject_MakeTpCall in /usr/bin/python3
184: 51# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 52# 0x000000000059582E in /usr/bin/python3
184: 53# _PyObject_MakeTpCall in /usr/bin/python3
184: 54# _PyEval_EvalFrameDefault in /usr/bin/python3
184: 55# PyEval_EvalCode in /usr/bin/python3
184: 56# 0x000000000066A861 in /usr/bin/python3
184: 57# 0x000000000066670C in /usr/bin/python3
184: 58# 0x000000000067F713 in /usr/bin/python3
184: 59# 0x000000000067ECE3 in /usr/bin/python3
184: 60# 0x000000000067EB1E in /usr/bin/python3
184: 61# Py_RunMain in /usr/bin/python3
184: 62# Py_BytesMain in /usr/bin/python3
184: 63# 0x00007F417A967CA8 in /lib/x86_64-linux-gnu/libc.so.6
184: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
184: 65# _start in /usr/bin/python3
184: ----------
184: ****
184:
152: .............[06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
194: ..[06:35:09]
194:
194: ****
194: Pre-condition Violation
194: no owner
194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
194: Failed Expression: dp_mol
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDKit::ROMol& (RDKit::Atom::*)() const, boost::python::return_internal_reference<1ul, boost::python::default_call_policies>, boost::mpl::vector2<RDKit::ROMol&, RDKit::Atom&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 5# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 16# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 26# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# _PyObject_MakeTpCall in /usr/bin/python3
194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 29# 0x00000000005BEE79 in /usr/bin/python3
194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 31# 0x0000000000547080 in /usr/bin/python3
194: 32# 0x00000000006AB720 in /usr/bin/python3
194: 33# _PyObject_MakeTpCall in /usr/bin/python3
194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 35# 0x00000000005BEE79 in /usr/bin/python3
194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 37# 0x0000000000547080 in /usr/bin/python3
194: 38# 0x00000000006AB720 in /usr/bin/python3
194: 39# _PyObject_MakeTpCall in /usr/bin/python3
194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 41# 0x00000000005BEE79 in /usr/bin/python3
194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 43# 0x0000000000547080 in /usr/bin/python3
194: 44# 0x00000000006AB720 in /usr/bin/python3
194: 45# _PyObject_MakeTpCall in /usr/bin/python3
194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 47# 0x000000000059582E in /usr/bin/python3
194: 48# _PyObject_MakeTpCall in /usr/bin/python3
194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 50# PyEval_EvalCode in /usr/bin/python3
194: 51# 0x000000000066A861 in /usr/bin/python3
194: 52# 0x000000000066670C in /usr/bin/python3
194: 53# 0x000000000067F713 in /usr/bin/python3
194: 54# 0x000000000067ECE3 in /usr/bin/python3
194: 55# 0x000000000067EB1E in /usr/bin/python3
194: 56# Py_RunMain in /usr/bin/python3
194: 57# Py_BytesMain in /usr/bin/python3
194: 58# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 60# _start in /usr/bin/python3
194: ----------
194: ****
194:
194: [06:35:09]
194:
194: ****
194: Pre-condition Violation
194: no owner
194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
194: Failed Expression: dp_mol
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<boost::python::tuple (*)(RDKit::Atom*), boost::python::default_call_policies, boost::mpl::vector2<boost::python::tuple, RDKit::Atom*> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 5# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 16# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 26# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# _PyObject_MakeTpCall in /usr/bin/python3
194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 29# 0x00000000005BEE79 in /usr/bin/python3
194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 31# 0x0000000000547080 in /usr/bin/python3
194: 32# 0x00000000006AB720 in /usr/bin/python3
194: 33# _PyObject_MakeTpCall in /usr/bin/python3
194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 35# 0x00000000005BEE79 in /usr/bin/python3
194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 37# 0x0000000000547080 in /usr/bin/python3
194: 38# 0x00000000006AB720 in /usr/bin/python3
194: 39# _PyObject_MakeTpCall in /usr/bin/python3
194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 41# 0x00000000005BEE79 in /usr/bin/python3
194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 43# 0x0000000000547080 in /usr/bin/python3
194: 44# 0x00000000006AB720 in /usr/bin/python3
194: 45# _PyObject_MakeTpCall in /usr/bin/python3
194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 47# 0x000000000059582E in /usr/bin/python3
194: 48# _PyObject_MakeTpCall in /usr/bin/python3
194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 50# PyEval_EvalCode in /usr/bin/python3
194: 51# 0x000000000066A861 in /usr/bin/python3
194: 52# 0x000000000066670C in /usr/bin/python3
194: 53# 0x000000000067F713 in /usr/bin/python3
194: 54# 0x000000000067ECE3 in /usr/bin/python3
194: 55# 0x000000000067EB1E in /usr/bin/python3
194: 56# Py_RunMain in /usr/bin/python3
194: 57# Py_BytesMain in /usr/bin/python3
194: 58# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 60# _start in /usr/bin/python3
194: ----------
194: ****
194:
194: [06:35:09]
194:
194: ****
194: Pre-condition Violation
194: no owner
194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
194: Failed Expression: dp_mol
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<boost::python::tuple (*)(RDKit::Atom*), boost::python::default_call_policies, boost::mpl::vector2<boost::python::tuple, RDKit::Atom*> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 5# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 16# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 26# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# _PyObject_MakeTpCall in /usr/bin/python3
194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 29# 0x00000000005BEE79 in /usr/bin/python3
194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 31# 0x0000000000547080 in /usr/bin/python3
194: 32# 0x00000000006AB720 in /usr/bin/python3
194: 33# _PyObject_MakeTpCall in /usr/bin/python3
194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 35# 0x00000000005BEE79 in /usr/bin/python3
194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 37# 0x0000000000547080 in /usr/bin/python3
194: 38# 0x00000000006AB720 in /usr/bin/python3
194: 39# _PyObject_MakeTpCall in /usr/bin/python3
194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 41# 0x00000000005BEE79 in /usr/bin/python3
194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 43# 0x0000000000547080 in /usr/bin/python3
194: 44# 0x00000000006AB720 in /usr/bin/python3
194: 45# _PyObject_MakeTpCall in /usr/bin/python3
194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 47# 0x000000000059582E in /usr/bin/python3
194: 48# _PyObject_MakeTpCall in /usr/bin/python3
194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 50# PyEval_EvalCode in /usr/bin/python3
194: 51# 0x000000000066A861 in /usr/bin/python3
194: 52# 0x000000000066670C in /usr/bin/python3
194: 53# 0x000000000067F713 in /usr/bin/python3
194: 54# 0x000000000067ECE3 in /usr/bin/python3
194: 55# 0x000000000067EB1E in /usr/bin/python3
194: 56# Py_RunMain in /usr/bin/python3
194: 57# Py_BytesMain in /usr/bin/python3
194: 58# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 60# _start in /usr/bin/python3
194: ----------
194: ****
194:
194: [06:35:09]
194:
194: ****
194: Pre-condition Violation
194: no owner
194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
194: Failed Expression: dp_mol
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<bool (*)(RDKit::Atom const*), boost::python::default_call_policies, boost::mpl::vector2<bool, RDKit::Atom const*> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 5# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 16# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 26# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# _PyObject_MakeTpCall in /usr/bin/python3
194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 29# 0x00000000005BEE79 in /usr/bin/python3
194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 31# 0x0000000000547080 in /usr/bin/python3
194: 32# 0x00000000006AB720 in /usr/bin/python3
194: 33# _PyObject_MakeTpCall in /usr/bin/python3
194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 35# 0x00000000005BEE79 in /usr/bin/python3
194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 37# 0x0000000000547080 in /usr/bin/python3
194: 38# 0x00000000006AB720 in /usr/bin/python3
194: 39# _PyObject_MakeTpCall in /usr/bin/python3
194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 41# 0x00000000005BEE79 in /usr/bin/python3
194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 43# 0x0000000000547080 in /usr/bin/python3
194: 44# 0x00000000006AB720 in /usr/bin/python3
194: 45# _PyObject_MakeTpCall in /usr/bin/python3
194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 47# 0x000000000059582E in /usr/bin/python3
194: 48# _PyObject_MakeTpCall in /usr/bin/python3
194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 50# PyEval_EvalCode in /usr/bin/python3
194: 51# 0x000000000066A861 in /usr/bin/python3
194: 52# 0x000000000066670C in /usr/bin/python3
194: 53# 0x000000000067F713 in /usr/bin/python3
194: 54# 0x000000000067ECE3 in /usr/bin/python3
194: 55# 0x000000000067EB1E in /usr/bin/python3
194: 56# Py_RunMain in /usr/bin/python3
194: 57# Py_BytesMain in /usr/bin/python3
194: 58# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 60# _start in /usr/bin/python3
194: ----------
194: ****
194:
194: [06:35:09]
194:
194: ****
194: Pre-condition Violation
194: no owner
194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h
194: Failed Expression: dp_mol
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<bool (*)(RDKit::Atom const*, int), boost::python::default_call_policies, boost::mpl::vector3<bool, RDKit::Atom const*, int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 5# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 16# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 26# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# _PyObject_MakeTpCall in /usr/bin/python3
194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 29# 0x00000000005BEE79 in /usr/bin/python3
194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 31# 0x0000000000547080 in /usr/bin/python3
194: 32# 0x00000000006AB720 in /usr/bin/python3
194: 33# _PyObject_MakeTpCall in /usr/bin/python3
194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 35# 0x00000000005BEE79 in /usr/bin/python3
194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 37# 0x0000000000547080 in /usr/bin/python3
194: 38# 0x00000000006AB720 in /usr/bin/python3
194: 39# _PyObject_MakeTpCall in /usr/bin/python3
194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 41# 0x00000000005BEE79 in /usr/bin/python3
194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 43# 0x0000000000547080 in /usr/bin/python3
194: 44# 0x00000000006AB720 in /usr/bin/python3
194: 45# _PyObject_MakeTpCall in /usr/bin/python3
194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 47# 0x000000000059582E in /usr/bin/python3
194: 48# _PyObject_MakeTpCall in /usr/bin/python3
194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 50# PyEval_EvalCode in /usr/bin/python3
194: 51# 0x000000000066A861 in /usr/bin/python3
194: 52# 0x000000000066670C in /usr/bin/python3
194: 53# 0x000000000067F713 in /usr/bin/python3
194: 54# 0x000000000067ECE3 in /usr/bin/python3
194: 55# 0x000000000067EB1E in /usr/bin/python3
194: 56# Py_RunMain in /usr/bin/python3
194: 57# Py_BytesMain in /usr/bin/python3
194: 58# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 60# _start in /usr/bin/python3
194: ----------
194: ****
194:
194: .....[06:35:09]
194:
194: ****
194: Range Error
194: atomIdx1
194: Violation occurred on line 496 in file ./Code/GraphMol/RWMol.cpp
194: Failed Expression: 0 < 0
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<int (RDKit::ReadWriteMol::*)(unsigned int, unsigned int, RDKit::Bond::BondType), boost::python::default_call_policies, boost::mpl::vector5<int, RDKit::ReadWriteMol&, unsigned int, unsigned int, RDKit::Bond::BondType> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 5# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 16# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 26# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# _PyObject_MakeTpCall in /usr/bin/python3
194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 29# 0x00000000005BEE79 in /usr/bin/python3
194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 31# 0x0000000000547080 in /usr/bin/python3
194: 32# 0x00000000006AB720 in /usr/bin/python3
194: 33# _PyObject_MakeTpCall in /usr/bin/python3
194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 35# 0x00000000005BEE79 in /usr/bin/python3
194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 37# 0x0000000000547080 in /usr/bin/python3
194: 38# 0x00000000006AB720 in /usr/bin/python3
194: 39# _PyObject_MakeTpCall in /usr/bin/python3
194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 41# 0x00000000005BEE79 in /usr/bin/python3
194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 43# 0x0000000000547080 in /usr/bin/python3
194: 44# 0x00000000006AB720 in /usr/bin/python3
194: 45# _PyObject_MakeTpCall in /usr/bin/python3
194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 47# 0x000000000059582E in /usr/bin/python3
194: 48# _PyObject_MakeTpCall in /usr/bin/python3
194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 50# PyEval_EvalCode in /usr/bin/python3
194: 51# 0x000000000066A861 in /usr/bin/python3
194: 52# 0x000000000066670C in /usr/bin/python3
194: 53# 0x000000000067F713 in /usr/bin/python3
194: 54# 0x000000000067ECE3 in /usr/bin/python3
194: 55# 0x000000000067EB1E in /usr/bin/python3
194: 56# Py_RunMain in /usr/bin/python3
194: 57# Py_BytesMain in /usr/bin/python3
194: 58# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 60# _start in /usr/bin/python3
194: ----------
194: ****
194:
194: ......[06:35:09] SMILES Parse Error: unclosed ring for input: 'c1ccccc'
194: [06:35:09] ERROR: Smiles parse error on line 0
194: [06:35:09] ERROR: Cannot create molecule from : 'c1ccccc'
194: [06:35:09] SMILES Parse Error: extra open parentheses while parsing: C(C
194: [06:35:09] SMILES Parse Error: check for mistakes around position 2:
194: [06:35:09] C(C
194: [06:35:09] ~^
194: [06:35:09] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C'
194: [06:35:09] ERROR: Smiles parse error on line 3
194: [06:35:09] ERROR: Cannot create molecule from : 'C(C'
194: [06:35:09] Explicit valence for atom # 1 C, 5, is greater than permitted
194: [06:35:09] ERROR: Could not sanitize molecule on line 6
194: [06:35:09] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted
194: [06:35:09] SMILES Parse Error: unclosed ring for input: 'c1ccccc'
194: [06:35:09] ERROR: Smiles parse error on line 0
194: [06:35:09] ERROR: Cannot create molecule from : 'c1ccccc'
194: [06:35:09] SMILES Parse Error: extra open parentheses while parsing: C(C
194: [06:35:09] SMILES Parse Error: check for mistakes around position 2:
194: [06:35:09] C(C
194: [06:35:09] ~^
194: [06:35:09] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C'
194: [06:35:09] ERROR: Smiles parse error on line 3
194: [06:35:09] ERROR: Cannot create molecule from : 'C(C'
194: [06:35:09] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC'
194: [06:35:09] ERROR: Smiles parse error on line 6
194: [06:35:09] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC'
194: [06:35:09] Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] ERROR: Could not sanitize molecule ending on line 21
194: [06:35:09] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] ERROR: EOF hit while reading atoms
194: [06:35:09] ERROR: moving to the beginning of the next molecule
194: [06:35:09] Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] ERROR: Could not sanitize molecule ending on line 21
194: [06:35:09] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] ERROR: EOF hit while reading atoms
194: [06:35:09] ERROR: moving to the beginning of the next molecule
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
194: ....[06:35:09]
194:
194: ****
194: Pre-condition Violation
194: RingInfo not initialized
194: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp
194: Failed Expression: df_init
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<unsigned int (RDKit::RingInfo::*)() const, boost::python::default_call_policies, boost::mpl::vector2<unsigned int, RDKit::RingInfo&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 5# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 16# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 26# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# _PyObject_MakeTpCall in /usr/bin/python3
194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 29# 0x00000000005BEE79 in /usr/bin/python3
194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 31# 0x0000000000547080 in /usr/bin/python3
194: 32# 0x00000000006AB720 in /usr/bin/python3
194: 33# _PyObject_MakeTpCall in /usr/bin/python3
194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 35# 0x00000000005BEE79 in /usr/bin/python3
194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 37# 0x0000000000547080 in /usr/bin/python3
194: 38# 0x00000000006AB720 in /usr/bin/python3
194: 39# _PyObject_MakeTpCall in /usr/bin/python3
194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 41# 0x00000000005BEE79 in /usr/bin/python3
194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 43# 0x0000000000547080 in /usr/bin/python3
194: 44# 0x00000000006AB720 in /usr/bin/python3
194: 45# _PyObject_MakeTpCall in /usr/bin/python3
194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 47# 0x000000000059582E in /usr/bin/python3
194: 48# _PyObject_MakeTpCall in /usr/bin/python3
194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 50# PyEval_EvalCode in /usr/bin/python3
194: 51# 0x000000000066A861 in /usr/bin/python3
194: 52# 0x000000000066670C in /usr/bin/python3
194: 53# 0x000000000067F713 in /usr/bin/python3
194: 54# 0x000000000067ECE3 in /usr/bin/python3
194: 55# 0x000000000067EB1E in /usr/bin/python3
194: 56# Py_RunMain in /usr/bin/python3
194: 57# Py_BytesMain in /usr/bin/python3
194: 58# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 60# _start in /usr/bin/python3
194: ----------
194: ****
194:
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
194: .............[06:35:09]
194:
194: ****
194: Range Error
194: idx
194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp
194: Failed Expression: 3 < 1
194: ----------
194: Stacktrace:
194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1
194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1
194: 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<RDKit::Atom* (RDKit::ROMol::*)(unsigned int), boost::python::return_internal_reference<1ul, boost::python::with_custodian_and_ward_postcall<0ul, 1ul, boost::python::default_call_policies> >, boost::mpl::vector3<RDKit::Atom*, RDKit::ROMol&, unsigned int> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 5# 0x00007F5675CA662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::SLNParseException, void (*)(RDKit::SLNParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::SLNParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so
194: 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionException, void (*)(RDKit::ChemicalReactionException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ChemicalReactionParserException, void (*)(RDKit::ChemicalReactionParserException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ChemicalReactionParserException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so
194: 10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FeatureFileParseException, void (*)(RDKit::FeatureFileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FeatureFileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so
194: 11# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDDepict::DepictException, void (*)(RDDepict::DepictException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDDepict::DepictException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so
194: 12# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 13# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so
194: 14# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so
194: 15# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 16# 0x00007F56733B69C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 17# 0x00007F56733B6993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 18# 0x00007F56733B6963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 19# 0x00007F56733B6933 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 20# 0x00007F56733B6903 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so
194: 21# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 22# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 23# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 24# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so
194: 25# boost::python::handle_exception_impl(boost::function0<void>) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 26# 0x00007F5675CA33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0
194: 27# _PyObject_MakeTpCall in /usr/bin/python3
194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 29# 0x00000000005BEE79 in /usr/bin/python3
194: 30# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 31# 0x0000000000547080 in /usr/bin/python3
194: 32# 0x00000000006AB720 in /usr/bin/python3
194: 33# _PyObject_MakeTpCall in /usr/bin/python3
194: 34# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 35# 0x00000000005BEE79 in /usr/bin/python3
194: 36# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 37# 0x0000000000547080 in /usr/bin/python3
194: 38# 0x00000000006AB720 in /usr/bin/python3
194: 39# _PyObject_MakeTpCall in /usr/bin/python3
194: 40# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 41# 0x00000000005BEE79 in /usr/bin/python3
194: 42# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 43# 0x0000000000547080 in /usr/bin/python3
194: 44# 0x00000000006AB720 in /usr/bin/python3
194: 45# _PyObject_MakeTpCall in /usr/bin/python3
194: 46# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 47# 0x000000000059582E in /usr/bin/python3
194: 48# _PyObject_MakeTpCall in /usr/bin/python3
194: 49# _PyEval_EvalFrameDefault in /usr/bin/python3
194: 50# PyEval_EvalCode in /usr/bin/python3
194: 51# 0x000000000066A861 in /usr/bin/python3
194: 52# 0x000000000066670C in /usr/bin/python3
194: 53# 0x000000000067F713 in /usr/bin/python3
194: 54# 0x000000000067ECE3 in /usr/bin/python3
194: 55# 0x000000000067EB1E in /usr/bin/python3
194: 56# Py_RunMain in /usr/bin/python3
194: 57# Py_BytesMain in /usr/bin/python3
194: 58# 0x00007F5676480CA8 in /lib/x86_64-linux-gnu/libc.so.6
194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6
194: 60# _start in /usr/bin/python3
194: ----------
194: ****
194:
194: ...[06:35:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:09] Molecule does not have explicit Hs. Consider calling AddHs()
194: ............................[06:35:09] SMILES Parse Error: unclosed ring for input: 'C1CC'
194: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8|
194: 837
194: ..[06:35:09] WARNING: not removing hydrogen atom without neighbors
194: [06:35:09] WARNING: not removing hydrogen atom with dummy atom neighbors
194: [06:35:09] WARNING: not removing hydrogen atom with wedged bond
194: [06:35:09] WARNING: not removing hydrogen atom without neighbors
194: [06:35:09] WARNING: not removing hydrogen atom with dummy atom neighbors
194: ......[06:35:09] Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] Can't kekulize mol. Unkekulized atoms: 0 1 2
194: .[06:35:09] Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] Explicit valence for atom # 1 F, 2, is greater than permitted
194: [06:35:09] Can't kekulize mol. Unkekulized atoms: 0 1 2
194: [06:35:09] Can't kekulize mol. Unkekulized atoms: 0 1 2
194: [06:35:09] Can't kekulize mol. Unkekulized atoms: 0 1 2
194: ..........[06:35:09] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname
194: [06:35:09] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname'
194: .[06:35:09] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname
194: [06:35:09] SMILES Parse Error: check for mistakes around position 4:
194: [06:35:09] CCC |$foo;;bar$| ourname
194: [06:35:09] ~~~^
194: [06:35:09] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname'
194: ..[06:35:09] SMILES Parse Error: syntax error while parsing: error
194: [06:35:09] SMILES Parse Error: check for mistakes around position 1:
194: [06:35:09] error
194: [06:35:09] ^
194: [06:35:09] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error'
194: [06:35:09] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd'
194: [06:35:09] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error'
194: [06:35:09] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd'
194: .........................[06:35:09] SMILES Parse Error: syntax error while parsing: garbage_0
194: [06:35:09] SMILES Parse Error: check for mistakes around position 1:
194: [06:35:09] garbage_0
194: [06:35:09] ^
194: [06:35:09] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0'
194: [06:35:09] SMILES Parse Error: syntax error while parsing: garbage_2
194: [06:35:09] SMILES Parse Error: check for mistakes around position 1:
194: [06:35:09] garbage_2
194: [06:35:09] ^
194: [06:35:09] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2'
194: [06:35:09] SMILES Parse Error: syntax error while parsing: garbage_4
194: [06:35:09] SMILES Parse Error: check for mistakes around position 1:
194: [06:35:09] garbage_4
194: [06:35:09] ^
194: [06:35:09] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4'
194: ............
194: ----------------------------------------------------------------------
194: Ran 279 tests in 10.740s
194:
194: OK
194: supplier: <class 'rdkit.Chem.rdmolfiles.SmilesMolSupplier'>
194: supplier: <class 'rdkit.Chem.rdmolfiles.SDMolSupplier'>
194: supplier: <class 'rdkit.Chem.rdmolfiles.TDTMolSupplier'>
218/235 Test #194: pyGraphMolWrap ......................... Passed 11.47 sec
173: Query 0
95: 0,0 0
95: 0,1 0
95: 1,0 0
95: 1,1 0
95: 2,0 0
95: 2,1 0
219/235 Test #95: testEnumeration ........................ Passed 15.47 sec
29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log...
184: .............
184: ----------------------------------------------------------------------
184: Ran 19 tests in 13.030s
184:
184: OK
184: Testing atom rings
184: testing bond rings
184: searching atom rings
184: searching bond rings
184: done
29: All 191 tests passed
29: done
29: -------------------------------------
29: Unit tests for all MMFF constraint terms.
220/235 Test #184: pySubstructLibrary ..................... Passed 13.60 sec
29: 10.0003
29: done
29: -------------------------------------
29: Unit test for MMFF TorsionConstraint close to 0 degrees.
29: done
29: -------------------------------------
29: Unit tests for copying MMFF ForceFields.
29: done
29: -------------------------------------
29: Unit test for MMFF butane scan.
29: done
221/235 Test #29: testMMFFForceField ..................... Passed 16.68 sec
152: ...[06:35:11] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:11] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:11] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:11] Molecule does not have explicit Hs. Consider calling AddHs()
152: [06:35:11] Molecule does not have explicit Hs. Consider calling AddHs()
163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds
163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds
163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds
163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds
163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds
163: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds
163: TOTAL Time elapsed 15.45 seconds
152: ...
152: ----------------------------------------------------------------------
152: Ran 19 tests in 15.396s
152:
152: OK
152: Testing MolAlign Wrappers
222/235 Test #163: testFMCS ............................... Passed 15.51 sec
223/235 Test #152: pyMolAlign ............................. Passed 15.75 sec
52: Randomness seeded to: 558554392
52: ===============================================================================
52: All tests passed (14835 assertions in 14 test cases)
52:
224/235 Test #52: canonTestsCatch ........................ Passed 17.92 sec
173: Query 1
150: ---------------------------------
150: test O3A multithreading bug
150:
150: ---------------------------------
150: testCrippenO3A multithreading
150:
150: generating reference data
150: processing
150: launch :0
150: launch :1
150: launch :2
150: launch :3
173: Query 2
148: .........[06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: .[06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: .[06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
148: [06:35:14] Molecule does not have explicit Hs. Consider calling AddHs()
209: [06:35:15] Explicit valence for atom # 0 Br, 1, is greater than permitted
209: ===============================================================================
209: All tests passed (38344 assertions in 51 test cases)
209:
225/235 Test #209: molStandardizeCatchTest ................ Passed 16.05 sec
148: ...
148: ----------------------------------------------------------------------
148: Ran 22 tests in 20.993s
148:
148: OK
226/235 Test #148: pyDistGeomHelpers ...................... Passed 21.36 sec
33: [06:35:17] Finished
33: [06:35:17] -------------------------------------
33: [06:35:17] Test github1843: RWMol.clear() should not destroy ring pointer.
33: [06:35:17] Finished
33: [06:35:17] -------------------------------------
33: [06:35:17] Test Github 6370: non-physical radical counts being preserved
33: [06:35:17] Finished
227/235 Test #33: graphmolTest1 .......................... Passed 22.79 sec
235: DbCLI/UnitTestDbCLI.py ............ [100%]
235:
235: =============================== warnings summary ===============================
235: ../obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20
235: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
235: decBase = declarative_base()
235:
235: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
235: ======================== 12 passed, 1 warning in 17.81s ========================
228/235 Test #235: pythonProjectTests ..................... Passed 18.35 sec
5: [06:35:21] Finished: testMultipleTimes()
5: [06:35:21]
5: -----------------------------------------
229/235 Test #5: testConcurrentQueue .................... Passed 26.26 sec
150: ---------------------------------
150: test getO3AForProbeConfs
150:
150: ***********************************************************
230/235 Test #150: testO3AAlign ........................... Passed 25.20 sec
147: [06:35:26] UFFTYPER: Unrecognized atom type: S_6+6 (0)
147: [06:35:26] UFFTYPER: Warning: hybridization set to SP3 for atom 0
147: [06:35:26] UFFTYPER: Unrecognized charge state for atom: 0
146: [06:35:33] done
171: ===============================================================================
171: All tests passed (93 assertions in 5 test cases)
171:
231/235 Test #171: testRascalCluster ...................... Passed 38.12 sec
146: [06:35:33] ---------------------------------
146: [06:35:33] test github issue 256: handling of zero-atom molecules
146:
146: [06:35:33] ---------------------------------
146: [06:35:33] test embedder callback function
146: [06:35:33] ---------------------------------
146: [06:35:33] test multi-threaded multi-conf embedding
146:
146: [06:35:36] ---------------------------------
146: [06:35:36] test github issue 563: Incorrect ring stereochemistry after embedding
146:
146: CNC[C@H]1CC[C@H](C[NH3+])CC1
173: Query 3
146: [06:35:37] ---------------------------------
146: [06:35:37] test github issue 568: Incorrect stereochemistry after embedding
146:
146: C1=NC[C@]2(CN3CC[C@@H]2C3)O1
146: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2
173: Query 4
146: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12
146: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21
146: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O
146: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O
146: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O
146: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O
146: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC
146: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O
146: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21
146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2
146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21
146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2
146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1
146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O
146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O
146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O
170: ===============================================================================
170: All tests passed (3582 assertions in 34 test cases)
170:
232/235 Test #170: testRascalMCES ......................... Passed 50.23 sec
146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3
173: Query 5
146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5
146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2
147: [06:35:48] Interrupted, cancelling conformer generation
147: Atoms:
147: 0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[9 3 1 6]
147: 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[0 13 6 7]
147: 2 7 N chg: 0 deg: 3 exp: 3 imp: 0 hyb: SP2 arom?: 1
147: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2
147: 4 7 N chg: 0 deg: 1 exp: 1 imp: 2 hyb: SP3
147: 5 6 C chg: 0 deg: 3 exp: 3 imp: 1 hyb: SP3 chi: CW nbrs:[4 11 7]
147: 6 7 N chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 rad: 1
147: 7 7 N chg: 0 deg: 2 exp: 2 imp: 1 hyb: SP3
147: 8 7 N chg: 0 deg: 3 exp: 3 imp: 0 hyb: SP2 arom?: 1
147: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP3
147: 10 8 O chg: 0 deg: 1 exp: 2 imp: 0 hyb: SP2
147: 11 7 N chg: 0 deg: 2 exp: 2 imp: 1 hyb: SP2
147: 12 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1
147: 13 8 O chg: 0 deg: 1 exp: 1 imp: 0 hyb: SP3 rad: 1
147: Bonds:
147: 0 0->9 order: 1
147: 1 0->3 order: 1
147: 2 1->0 order: 1
147: 3 1->13 order: 1
147: 4 2->8 order: a conj?: 1 aromatic?: 1
147: 5 2->12 order: a conj?: 1 aromatic?: 1
147: 6 3->10 order: 2 conj?: 1
147: 7 3->8 order: 1 conj?: 1
147: 8 5->4 order: 1
147: 9 11->5 order: 1
147: 10 6->1 order: 1
147: 11 6->0 order: 1
147: 12 7->1 order: 1
147: 13 7->5 order: 1
147: 14 8->12 order: a conj?: 1 aromatic?: 1
147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1
147: ===============================================================================
147: All tests passed (12742 assertions in 21 test cases)
147:
233/235 Test #147: distGeomHelpersCatch ................... Passed 53.04 sec
146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5
146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1
146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1
146: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1
146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13
146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12
146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-]
146: [06:35:58] Molecule does not have explicit Hs. Consider calling AddHs()
146: [06:35:53] ---------------------------------
146: [06:35:53] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system
146: [06:35:53] ---------------------------------
146: [06:35:53] More ChEMBL molecules failing bounds smoothing.
146: [06:35:53] ---------------------------------
146: [06:35:53] ugly conformations can be generated for highly constrained ring systems.
146: [06:35:53] ---------------------------------
146: [06:35:53] test embed parameters structure.
146: [06:35:53] ---------------------------------
146: [06:35:53] test github 1227: Hs being used in RMSD filtering.
146: [06:35:53] ---------------------------------
146: [06:35:53] Failure to embed larger aromatic rings.
146: [06:35:54] ---------------------------------
146: [06:35:54] Deterministic with large random seeds
146: [06:35:57] ---------------------------------
146: [06:35:57] Github #1990: seg fault after RemoveHs
146: [06:35:57] ---------------------------------
146: [06:35:57] Github #2246: Use coordMap when starting embedding from random coords
146: [06:35:58] ---------------------------------
146: [06:35:58] Providing a distance bounds matrix.
146: [06:35:58] ---------------------------------
146: [06:35:58] Disabling fragmentation.
146: [06:35:58] ---------------------------------
146: [06:35:58] Using symmetry in conformation pruning.
146: [06:35:58] ---------------------------------
146: [06:35:58] Force trans amides.
146: [06:35:58] ---------------------------------
146: [06:35:58] test missing Hs warning.
146: [06:35:58] ---------------------------------
146: [06:35:58] basic H bond support.
146: [06:35:58] *******************************************************
234/235 Test #146: testDistGeomHelpers .................... Passed 62.62 sec
173: ===============================================================================
173: All tests passed (215 assertions in 18 test cases)
173:
235/235 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 64.88 sec
100% tests passed, 0 tests failed out of 235
Total Test time (real) = 66.78 sec
make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6'
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
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dh_auto_install
cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/rdkit-202409.6/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
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make -f CMakeFiles/Makefile2 preinstall
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make[3]: Nothing to be done for 'preinstall'.
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Install the project...
/usr/bin/cmake -P cmake_install.cmake
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/DbMolSupplier.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Torsions.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Sheridan.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Utils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Pairs.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/BRICS.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/TorsionFingerprints.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FilterCatalog.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/GraphDescriptors.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Crippen.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Lipinski.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapParser.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMaps.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemicalForceFields.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FragmentMatcher.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PropertyMol.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FunctionalGroups.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/RegistrationHash.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/github4823.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolCatalog.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors3D.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ShowMols.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/BuilderUtils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeObjects.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/demoCombined.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeAligner.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/TemplateAlign.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/TemplateExpand.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/SDFToCSV.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/BulkTester.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/AlignDepict.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/ShowFeats.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/FeatDirUtilsRD.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/DSViewer.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FragmentCatalog.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MACCSkeys.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FastSDMolSupplier.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AllChem.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/EmbedLib.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/Pharmacophore.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MCS.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/InchiInfo.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/MolKey.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Graphs.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolSurf.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SaltRemover.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fragments.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/IPythonConsole.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/MolDrawing.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/FreeSans.ttf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/SimilarityMaps.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/InteractiveRenderer.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Recap.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/inchi.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_sa.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_orig.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Stats.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/MLData.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/DataUtils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/SplitData.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Transforms.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/FindQuantBounds.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Quantize.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/Risk.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/Scoring.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Parser.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Descriptors.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MatOps.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterVis.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/murtagh_test.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clusters.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Resemblance.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgeom.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgen.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfdoc.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfutils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pidtest.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pstests.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/testallps.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pidPIL.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/formatted-strings.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/pidTK.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWxDc.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/README
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/HierarchyVis.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/VectCollection.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/TopNContainer.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/LazySignature.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitUtils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsemble.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsembleDb.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/pytest.ini
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Transform.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Node.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/demo.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Filter.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDConfig.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbResultSet.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbInfo.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbModule.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbConnection.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbUtils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/StorageUtils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDLogger.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/conftest.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/DTDs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/RDData.sqlt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/NCI
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/test_data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/rddata.sql
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Salts.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/struchk
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Crippen.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_13.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images/logo.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images/wiki
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/Chem
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/CIPLabeling.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/SGroups.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/RD.css
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/RDKit_Book.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/Install.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/index.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/exts
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/exts/extapi.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmartsRemover.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.MoleculeDescriptors.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Standardize.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdDetermineBonds.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdCoordGen.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.SimilarityPickers.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolCatalog.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.Sheridan.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolAlign.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.Loader.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Clusters.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Avalon.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.DataUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Numerics.rdAlignment.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdFingerprintGenerator.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdCIPLabeler.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Node.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolStandardize.rdMolStandardize.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Generate.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Clustering.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.MLUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdFMCS.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.fmcs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdchem.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SATIS.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.DbPickleSupplier.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdSynthonSpaceSearch.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FastSDMolSupplier.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Features.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdDistGeom.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FragmentCatalog.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolEnumerator.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.MatOps.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdinchi.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.TemplateAlign.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.rdScaffoldNetwork.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SimpleEnum.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbConnection.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.ClusterMols.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Geometry.rdGeometry.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Descriptors3D.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.SLT.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Murtagh.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DistanceGeometry.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Utils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.SplitData.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatFinderCLI.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemicalFeatures.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.TopNContainer.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.cactvs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.BulkTester.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.DbMolSupplier.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.TemplateExpand.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.RegistrationHash.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolCatalog.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.TestRunner.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolKey.MolKey.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMapUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.EState.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdShapeAlign.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesSupply.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.fileutils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.entropy.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AllChem.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.SubshapeObjects.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.SimilarityMaps.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.BitEnsemble.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SDSupply.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdqueries.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.MolSupplier.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SaltRemover.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Filter.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EnumerateHeterocycles.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemicalForceFields.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.rdMolDraw2D.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.DbFpSupplier.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Supply.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.BuildFragmentCatalog.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.FingerprintUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.StorageUtils.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.SigFactory.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMaps.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMHFPFingerprint.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdReducedGraphs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SimpleEnum.Enumerator.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdmolfiles.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.cDataStructs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.inchi.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbResultSet.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.FingerprintMols.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Numerics.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDRandom.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Output.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PeriodicTable.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.LazySignature.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PandasTools.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ReducedGraphs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FilterCatalog.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ForceField.rdForceField.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataManip.Metric.rdMetricMatrixCalc.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.Transforms.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.BitEnsembleDb.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdAbbreviations.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.Descriptors.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.EState_VSA.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PyMol.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.rdSimDivPickers.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.EmbedLib.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.Parser.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.BitUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Graphs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.rdMolDraw2DQt.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.Loader_sa.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Features.FeatDirUtilsRD.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fraggle.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fragments.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.MolDrawing.rst
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-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.BuilderUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.SubshapeBuilder.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Crippen.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.DbMolSupply.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DistanceGeometry.DistGeom.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.ClusterUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDLogger.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Matcher.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.fmcs.fmcs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Transform.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.ClusterVis.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Lipinski.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDPaths.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMapParser.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataManip.Metric.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Butina.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.CompoundDescriptors.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.TorsionFingerprints.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.DescriptorUtilities.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesOutput.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdtrajectory.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdShapeHelpers.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdfragcatalog.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FunctionalGroups.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.BitClusterer.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbUtils.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Avalon.pyAvalonTools.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.Quantize.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Scoring.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.MLData.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.spiral.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.MolSimilarity.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.AlignDepict.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.MurckoScaffold.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Geometry.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example8.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example11.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example9.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example17.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example1.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example3.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example4.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example13.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example6.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example12.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example15.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example5.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example16.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example10.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example2.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example14.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example7.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedWithContributing.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/Makefile
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/conf.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/api-docs.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/Cookbook.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInC++.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/Cartridge.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInPython.rst
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp4.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_40_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/style.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_4.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_40_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_38_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_8.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/pull_req2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_4.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/rdkit_fork_clone.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/pull_req1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example5.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_39_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example4.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_5.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation1.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Glare
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/efgs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/efgs/efgs.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/efgs/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/efgs/ch33query.sql
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/efgs/try_efgs.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/M_Kossner
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NP_Score
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/testData
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/README
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/MolVS
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/IFG
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/IFG/README
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/build_sascore_db.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/pzc
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/.gitignore
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/CACHEDIR.TAG
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/stepwise
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/nodeids
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/AtomPairs.sqlt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/UnitTestDbCLI.cpython-313-pytest-8.3.4.pyc
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/CreateDb.cpython-313.pyc
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/SearchDb.cpython-313.pyc
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/UnitTestDbCLI.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/pytest.ini
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/test.sh
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__init__.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/README.md
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/license.txt
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDInchiLib.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/inchi.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdinchi.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/CoordGen.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdCoordGen.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitga.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitga.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitga.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDGeneral.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDGeneral.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDGeneral.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/Exceptions.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/BadFileException.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/BoostStartInclude.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/BoostEndInclude.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/ControlCHandler.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/Dict.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/FileParseException.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/Invariant.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDAny.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDValue.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDValue-doublemagic.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDValue-taggedunion.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDLog.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDProps.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDThreads.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/StreamOps.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/types.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/utils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/versions.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDConfig.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/LocaleSwitcher.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/Ranking.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/hanoiSort.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/RDExportMacros.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/export.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/test.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/ConcurrentQueue.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/hash
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDBoost.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDBoost.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDBoost/Wrap.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDBoost/PySequenceHolder.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDBoost/list_indexing_suite.hpp
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDBoost/python.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDBoost/boost_numpy.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDBoost/python_streambuf.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDBoost/pyint_api.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/rdBase.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDStreams.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDStreams.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDStreams.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/RDStreams/streams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDataStructs.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDataStructs.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDataStructs.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/base64.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/BitOps.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/BitVect.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/BitVects.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/BitVectUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/DatastructsException.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/DatastructsStreamOps.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/DiscreteDistMat.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/DiscreteValueVect.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/RealValueVect.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/ExplicitBitVect.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/SparseBitVect.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/SparseIntVect.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/FPBReader.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataStructs/MultiFPBReader.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/cDataStructs.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDGeometryLib.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDGeometryLib.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRDGeometryLib.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/Grid3D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/GridUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/point.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/Transform2D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/Transform3D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/Transform.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/UniformGrid3D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/UniformRealValueGrid3D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Geometry/Utils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry/rdGeometry.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAlignment.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAlignment.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAlignment.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/Alignment/AlignPoints.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/rdAlignment.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitEigenSolvers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/EigenSolvers/PowerEigenSolver.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitOptimizer.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitOptimizer.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitOptimizer.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/Optimizer/BFGSOpt.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/Matrix.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/SquareMatrix.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/SymmMatrix.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/Vector.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/Conrec.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/Contrib.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/ForceField.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/AngleConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/AngleConstraints.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraints.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/PositionConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/TorsionConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/PositionConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Nonbonded.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Params.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Utils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversion.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversions.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/rdForceField.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContrib.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContribs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContrib.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContribs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContrib.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContribs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/DistGeom.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Atom.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Atropisomers.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Bond.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Canon.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/details.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Rings.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/CanonicalizeStereoGroups.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDepictor.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MarvinParse/MarvinParser.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/CDXMLParser.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileWriters.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.v1API.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/GenericGroups/GenericGroups.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdChemReactions.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdTautomerQuery.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdfiltercatalog.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdfragcatalog.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolSurf.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MQN.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Property.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AtomFeat.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/OxidationNumbers.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/DCLV.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/EEM.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PBF.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PMI.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RDF.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MORSE.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/GETAWAY.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/WHIM.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/CoulombMat.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolDescriptors.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/Fingerprints.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MACCS.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MHFP.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintGenerator.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairGenerator.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganGenerator.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdFingerprintGenerator.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMHFPFingerprint.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdPartialCharges.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolTransforms.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/FFConvenience.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/UFF.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdForceFieldHelpers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDistGeom.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolAlign.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolChemicalFeatures.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdShapeHelpers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolCatalog.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/rdMolDraw2D.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FMCS/FMCS.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdFMCS.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolHash.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMMPA.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalMCES.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalOptions.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalClusterOptions.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalResult.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdRascalMCES.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpace.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSet.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/Synthon.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SearchResults.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSynthonSpaceSearch.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/CIPLabeler/CIPLabeler.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/CIPLabeler/TooManyNodesException.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdCIPLabeler.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDeprotect.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdReducedGraphs.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructLibrary.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSubstructLibrary.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdRGroupDecomposition.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolInterchange.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSLNParse.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSLNParse.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSLNParse.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNAttribs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParse.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParseOps.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSLNParse.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdchem.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdmolops.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdqueries.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdmolfiles.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdtrajectory.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolStandardize.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolStandardize.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Pipeline.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolEnumerator.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/LinkNode.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolEnumerator.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdAbbreviations.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/GeneralizedSubstruct/XQMol.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdGeneralizedSubstruct.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolProcessing.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolProcessing.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolProcessing.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolProcessing/MolProcessing.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolProcessing.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInteractionFields.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInteractionFields.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInteractionFields.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolInteractionFields/MIFDescriptors.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMIF.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/AndQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/LessQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/OrQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/Query.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/QueryObjects.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/RangeQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/SetQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/XOrQuery.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Features/Feature.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clustering.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/cQuantize.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2024.09.6
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdChemicalFeatures.so
=====================================================================
PostgreSQL cartridge installation succeeded.
=====================================================================
Restart the PostgreSQL service before using the PostgreSQL
RDKit cartridge.
=====================================================================
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDPaths.py
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-targets.cmake
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-targets-none.cmake
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-config.cmake
-- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-config-version.cmake
make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu'
make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6'
mkdir -p /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3
mv /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3/dist-packages
rm -f -rf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13
ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf
dh_install -ppython3-rdkit /usr/lib/python3
rm -f -rf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/
rm -f -rf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/__pycache__
dh_numpy3
dh_install
for v in $(pg_buildext supported-versions); do \
mkdir -p debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/ debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \
cp Code/PgSQL/rdkit/build-$v/librdkit.so debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/rdkit.so; \
cp Code/PgSQL/rdkit/build-$v/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \
cp Code/PgSQL/rdkit/build-$v/update_sql/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \
cp Code/PgSQL/rdkit/rdkit.control debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \
done
mkdir -p /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/
# cp /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/
cp -a /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/
ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js
ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js
ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js
make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6'
dh_installdocs -O--buildsystem=cmake
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6'
dh_installchangelogs ReleaseNotes.md
make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6'
debian/rules override_dh_python3
make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6'
dh_python3 -ppython3-rdkit
I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdCoordGen.so to rdCoordGen.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdDepictor.so to rdDepictor.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdDeprotect.so to rdDeprotect.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdDistGeom.so to rdDistGeom.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdFMCS.so to rdFMCS.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdGeneralizedSubstruct.so to rdGeneralizedSubstruct.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMIF.so to rdMIF.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMMPA.so to rdMMPA.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolAlign.so to rdMolAlign.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolCatalog.so to rdMolCatalog.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolHash.so to rdMolHash.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolInterchange.so to rdMolInterchange.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolProcessing.so to rdMolProcessing.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolTransforms.so to rdMolTransforms.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdPartialCharges.so to rdPartialCharges.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdRascalMCES.so to rdRascalMCES.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdSLNParse.so to rdSLNParse.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdSynthonSpaceSearch.so to rdSynthonSpaceSearch.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdchem.so to rdchem.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdfragcatalog.so to rdfragcatalog.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdinchi.so to rdinchi.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdmolfiles.so to rdmolfiles.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdmolops.so to rdmolops.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdqueries.so to rdqueries.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdtrajectory.so to rdtrajectory.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-313-x86_64-linux-gnu.so
I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-313-x86_64-linux-gnu.so
dh_numpy3 -ppython3-rdkit
make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6'
dh_installsystemduser -O--buildsystem=cmake
dh_lintian -O--buildsystem=cmake
dh_perl -O--buildsystem=cmake
dh_link -O--buildsystem=cmake
dh_strip_nondeterminism -O--buildsystem=cmake
dh_compress -O--buildsystem=cmake
dh_fixperms -O--buildsystem=cmake
debian/rules override_dh_missing
make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6'
dh_missing --list-missing
dh_missing: warning: usr/lib/postgresql/17/lib/rdkit.so exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv exists in 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/GettingStartedWithContributing.md 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
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dh_missing: warning: usr/share/postgresql/17/extension/rdkit--3.8--4.0.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0--4.0.1.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0.1--4.1.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1--4.1.1.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1.1--4.2.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.2--4.3.0.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.3.0--4.4.0.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.4.0--4.5.0.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.5.0--4.6.0.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.0--4.6.1.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.1.sql exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/postgresql/17/extension/rdkit.control exists in debian/tmp but is not installed to anywhere
The following debhelper tools have reported what they installed (with files per package)
* dh_install: librdkit-dev (64), librdkit1t64 (124), postgresql-17-rdkit (0), python3-rdkit (1), rdkit-data (3), rdkit-doc (0)
* dh_installdocs: librdkit-dev (0), librdkit1t64 (0), postgresql-17-rdkit (0), python3-rdkit (0), rdkit-data (0), rdkit-doc (0)
If the missing files are installed by another tool, please file a bug against it.
When filing the report, if the tool is not part of debhelper itself, please reference the
"Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+).
(in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz)
Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built
If the omission is intentional or no other helper can take care of this consider adding the
paths to debian/not-installed.
make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6'
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: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol palloc0: it's probably a plugin
dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all)
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib64/ld-linux-x86-64.so.2
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged
dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries
dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all)
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib64/ld-linux-x86-64.so.2
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged
dh_installdeb -O--buildsystem=cmake
dh_gencontrol -O--buildsystem=cmake
dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined
dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined
dpkg-gencontrol: warning: package librdkit-dev: 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: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined
dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined
dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined
dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined
dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined
dh_md5sums -O--buildsystem=cmake
dh_builddeb -O--buildsystem=cmake
dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.6-2_amd64.deb'.
dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.6-2_amd64.deb'.
dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.6-2_all.deb'.
dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.6-2_all.deb'.
dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.6-2_amd64.deb'.
dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.6-2_amd64.deb'.
dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.6-2_amd64.deb'.
dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.6-2_amd64.deb'.
dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.6-2_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../rdkit_202409.6-2_amd64.buildinfo
dpkg-genchanges --build=binary -O../rdkit_202409.6-2_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/3364963/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/3364963/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/3364963 and its subdirectories
I: Current time: Mon Apr 20 06:40:45 +14 2026
I: pbuilder-time-stamp: 1776616845