I: pbuilder: network access will be disabled during build I: Current time: Sat Jul 11 00:21:40 +14 2020 I: pbuilder-time-stamp: 1594376500 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_201809.1+dfsg-6.dsc] I: copying [./rdkit_201809.1+dfsg.orig.tar.xz] I: copying [./rdkit_201809.1+dfsg-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Feb 1 03:20:34 2019 +14 gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rdkit_201809.1+dfsg-6.dsc dpkg-source: info: extracting rdkit in rdkit-201809.1+dfsg dpkg-source: info: unpacking rdkit_201809.1+dfsg.orig.tar.xz dpkg-source: info: unpacking rdkit_201809.1+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying NoDownloads.patch dpkg-source: info: applying postgres_v11_support.patch dpkg-source: info: applying postgres_Makefile_fixes.patch dpkg-source: info: applying postgres_disable_failing_tests.patch dpkg-source: info: applying sphinx_imgconverter.patch dpkg-source: info: applying catch2_header.patch dpkg-source: info: applying testcase_32bit_fix.patch dpkg-source: info: applying fix_coordgen_include_path.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9958/tmp/hooks/D01_modify_environment starting debug: Running on cbxi4b. 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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/9958/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/9958/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=773e10e299ea4eeca94c70462366baf2 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=9958 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/tmp.zyLF3MppoC/pbuilderrc_tdqH --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zyLF3MppoC/b2 --logfile b2/build.log rdkit_201809.1+dfsg-6.dsc' SUDO_GID=116 SUDO_UID=112 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 4.19.0-9-armmp #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash -rwxr-xr-x 1 root root 71648 Mar 1 2019 date -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd -rwxr-xr-x 1 root root 55672 Mar 1 2019 df -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 18260 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln -rwxr-xr-x 1 root root 34932 Jul 27 2018 login -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 10 2019 more -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 11 00:23 sh -> bash lrwxrwxrwx 1 root root 4 Jul 10 22:27 sh.distrib -> dash -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty -rwsr-xr-x 1 root root 42472 Jan 10 2019 su -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch -rwxr-xr-x 1 root root 18260 Mar 1 2019 true -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/9958/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: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bison, cmake, debhelper (>> 9), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libschroedinger-coordgenlibs-dev, libschroedinger-maeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python-dev, python-pil, python-numpy, python-pandas, python3-sphinx, python3-recommonmark, rapidjson-dev, texlive-fonts-recommended, texlive-generic-extra, 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 ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>> 9); however: Package debhelper 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-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 libschroedinger-coordgenlibs-dev; however: Package libschroedinger-coordgenlibs-dev is not installed. pbuilder-satisfydepends-dummy depends on libschroedinger-maeparser-dev; however: Package libschroedinger-maeparser-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 python-dev; however: Package python-dev is not installed. pbuilder-satisfydepends-dummy depends on python-pil; however: Package python-pil is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on python-pandas; however: Package python-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-recommonmark; however: Package python3-recommonmark is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev 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-generic-extra; however: Package texlive-generic-extra 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: adwaita-icon-theme{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bison{a} bsdmainutils{a} ca-certificates{a} clang-7{a} cmake{a} cmake-data{a} dbus{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} distro-info-data{a} dmsetup{a} docutils-common{a} doxygen{a} dwz{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} glib-networking{a} glib-networking-common{a} glib-networking-services{a} groff-base{a} gsettings-desktop-schemas{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} icu-devtools{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} latexmk{a} libapparmor1{a} libarchive-zip-perl{a} libarchive13{a} libargon2-1{a} libatk-bridge2.0-0{a} libatk1.0-0{a} libatk1.0-data{a} libatspi2.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbison-dev{a} libblas3{a} libboost-atomic1.67-dev{a} libboost-atomic1.67.0{a} libboost-chrono1.67-dev{a} libboost-chrono1.67.0{a} libboost-date-time1.67-dev{a} libboost-date-time1.67.0{a} libboost-dev{a} libboost-python-dev{a} libboost-python1.67-dev{a} libboost-python1.67.0{a} libboost-regex-dev{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-system-dev{a} libboost-system1.67-dev{a} libboost-thread-dev{a} libboost-thread1.67-dev{a} libboost-thread1.67.0{a} libboost1.67-dev{a} libbrotli1{a} libbsd0{a} libcairo-gobject2{a} libcairo2{a} libcap2{a} libclang-common-7-dev{a} libclang1-6.0{a} libclang1-7{a} libcolord2{a} libcroco3{a} libcryptsetup12{a} libcups2{a} libcupsimage2{a} libcurl4{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libde265-0{a} libdevmapper1.02.1{a} libedit2{a} libelf1{a} libepoxy0{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgc1c2{a} libgdk-pixbuf2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libgtk-3-0{a} libgtk-3-common{a} libharfbuzz-icu0{a} libharfbuzz0b{a} libheif1{a} libice6{a} libicu-dev{a} libicu63{a} libidn11{a} libijs-0.35{a} libimagequant0{a} libip4tc0{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-c3{a} libjson-glib-1.0-0{a} libjson-glib-1.0-common{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkmod2{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} libllvm6.0{a} libllvm7{a} liblqr-1-0{a} libltdl7{a} liblua5.1-0{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libmpdec2{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libobjc-8-dev{a} libobjc4{a} libopenjp2-7{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpotrace0{a} libpq-dev{a} libpq5{a} libprocps7{a} libproxy1v5{a} libpsl5{a} libptexenc1{a} libpython-dev{a} libpython-stdlib{a} libpython2-dev{a} libpython2-stdlib{a} libpython2.7{a} libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.7{a} libpython3.7-dev{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librest-0.7-0{a} librhash0{a} librsvg2-2{a} librsvg2-bin{a} librsvg2-common{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libschroedinger-coordgenlibs-dev{a} libschroedinger-coordgenlibs1{a} libschroedinger-maeparser-dev{a} libschroedinger-maeparser1{a} libsigsegv2{a} libsm6{a} libsoup-gnome2.4-1{a} libsoup2.4-1{a} libsqlite3-dev{a} libssh2-1{a} libssl1.1{a} libsynctex2{a} libteckit0{a} libtexlua52{a} libtexlua53{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtiff5{a} libtinfo-dev{a} libtool{a} libuchardet0{a} libuv1{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libwoff1{a} libx11-6{a} libx11-data{a} libx265-165{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml2{a} libxmu6{a} libxpm4{a} libxrandr2{a} libxrender1{a} libxt6{a} libxxhash0{a} libyaml-0-2{a} libzzip-0-13{a} llvm-7{a} llvm-7-dev{a} llvm-7-runtime{a} lsb-base{a} lsb-release{a} m4{a} man-db{a} mime-support{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} poppler-data{a} postgresql-client-common{a} postgresql-common{a} postgresql-server-dev-11{a} postgresql-server-dev-all{a} preview-latex-style{a} procps{a} python{a} python-babel-localedata{a} python-dateutil{a} python-dev{a} python-minimal{a} python-numpy{a} python-pandas{a} python-pandas-lib{a} python-pil{a} python-pkg-resources{a} python-six{a} python-tz{a} python2{a} python2-dev{a} python2-minimal{a} python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-commonmark-bkrs{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-pyparsing{a} python3-recommonmark{a} python3-requests{a} python3-roman{a} python3-six{a} python3-sphinx{a} python3-tz{a} python3-urllib3{a} python3.7{a} python3.7-dev{a} python3.7-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sphinx-common{a} ssl-cert{a} systemd{a} systemd-sysv{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-generic-extra{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} texlive-plain-generic{a} ucf{a} x11-common{a} xdg-utils{a} xkb-data{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: at-spi2-core atril curl evince fonts-droid-fallback ghostscript gsfonts gv javascript-common krb5-locales libarchive-cpio-perl libcupsfilters1 libfile-mimeinfo-perl libfl-dev libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgtk-3-bin libltdl-dev libmagickcore-6.q16-6-extra libmail-sendmail-perl libnet-dbus-perl libnss-systemd libomp-7-dev libsasl2-modules libx11-protocol-perl lmodern logrotate lynx mupdf netpbm okular psmisc publicsuffix python-bs4 python-html5lib python-lxml python-matplotlib python-numexpr python-olefile python-openpyxl python-scipy python-statsmodels python-tables python-xlrd python-xlwt python3-pil ruby tex-gyre tipa tk viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 355 newly installed, 0 to remove and 0 not upgraded. Need to get 405 MB of archives. After unpacking 1530 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libapparmor1 armhf 2.13.2-10 [89.6 kB] Get: 2 http://deb.debian.org/debian buster/main armhf libcap2 armhf 1:2.25-2 [16.3 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libargon2-1 armhf 0~20171227-0.2 [20.4 kB] Get: 4 http://deb.debian.org/debian buster/main armhf dmsetup armhf 2:1.02.155-3 [90.0 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libdevmapper1.02.1 armhf 2:1.02.155-3 [131 kB] Get: 6 http://deb.debian.org/debian buster/main armhf libjson-c3 armhf 0.12.1+ds-2 [24.9 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libcryptsetup12 armhf 2:2.1.0-5+deb10u2 [174 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libidn11 armhf 1.33-2.2 [113 kB] Get: 10 http://deb.debian.org/debian buster/main armhf libip4tc0 armhf 1.8.2-4 [68.1 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libkmod2 armhf 26-1 [46.4 kB] Get: 12 http://deb.debian.org/debian buster/main armhf systemd armhf 241-7~deb10u4 [3284 kB] Get: 13 http://deb.debian.org/debian buster/main armhf systemd-sysv armhf 241-7~deb10u4 [99.9 kB] Get: 14 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 15 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 17 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 22 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 23 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 24 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 26 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 29 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 33 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 35 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 36 http://deb.debian.org/debian buster/main armhf flex armhf 2.6.4-6.2 [438 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libfftw3-double3 armhf 3.3.8-2 [432 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 40 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 41 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 42 http://deb.debian.org/debian buster/main armhf fonts-dejavu-core all 2.37-1 [1068 kB] Get: 43 http://deb.debian.org/debian buster/main armhf fontconfig-config all 2.13.1-2 [280 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libfontconfig1 armhf 2.13.1-2 [328 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libde265-0 armhf 1.0.3-1+b1 [192 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libx265-165 armhf 2.9-4 [536 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libheif1 armhf 1.3.2-2~deb10u1 [107 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libjbig0 armhf 2.1-3.1+b2 [28.4 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [112 kB] Get: 50 http://deb.debian.org/debian buster/main armhf liblcms2-2 armhf 2.9-3 [119 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 52 http://deb.debian.org/debian buster/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.5 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libltdl7 armhf 2.4.6-9 [387 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libopenjp2-7 armhf 2.3.0-2+deb10u1 [143 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libwebp6 armhf 0.6.1-2 [229 kB] Get: 56 http://deb.debian.org/debian buster/main armhf libtiff5 armhf 4.1.0+git191117-2~deb10u1 [252 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libwebpmux3 armhf 0.6.1-2 [94.1 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libxcb1 armhf 1.13.1-2 [132 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libx11-data all 2:1.6.7-1 [298 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libx11-6 armhf 2:1.6.7-1 [698 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libxext6 armhf 2:1.3.3-1+b2 [48.1 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 66 http://deb.debian.org/debian buster/main armhf imagemagick-6-common all 8:6.9.10.23+dfsg-2.1 [200 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libmagickcore-6.q16-6 armhf 8:6.9.10.23+dfsg-2.1 [1642 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libmagickwand-6.q16-6 armhf 8:6.9.10.23+dfsg-2.1 [434 kB] Get: 69 http://deb.debian.org/debian buster/main armhf poppler-data all 0.4.9-2 [1473 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libpython3.7-minimal armhf 3.7.3-2+deb10u1 [582 kB] Get: 71 http://deb.debian.org/debian buster/main armhf python3.7-minimal armhf 3.7.3-2+deb10u1 [1465 kB] Get: 72 http://deb.debian.org/debian buster/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB] Get: 73 http://deb.debian.org/debian buster/main armhf libmpdec2 armhf 2.4.2-2 [69.3 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libpython3.7-stdlib armhf 3.7.3-2+deb10u1 [1660 kB] Get: 75 http://deb.debian.org/debian buster/main armhf python3.7 armhf 3.7.3-2+deb10u1 [330 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB] Get: 77 http://deb.debian.org/debian buster/main armhf python3 armhf 3.7.3-1 [61.5 kB] Get: 78 http://deb.debian.org/debian buster/main armhf sgml-base all 1.29 [14.8 kB] Get: 79 http://deb.debian.org/debian buster/main armhf tex-common all 6.11 [53.1 kB] Get: 80 http://deb.debian.org/debian buster/main armhf netbase all 5.6 [19.4 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libprocps7 armhf 2:3.3.15-2 [58.7 kB] Get: 83 http://deb.debian.org/debian buster/main armhf lsb-base all 10.2019051400 [28.4 kB] Get: 84 http://deb.debian.org/debian buster/main armhf procps armhf 2:3.3.15-2 [248 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libdbus-1-3 armhf 1.12.16-1 [190 kB] Get: 86 http://deb.debian.org/debian buster/main armhf dbus armhf 1.12.16-1 [217 kB] Get: 87 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 89 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 90 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 91 http://deb.debian.org/debian buster/main armhf libpam-systemd armhf 241-7~deb10u4 [195 kB] Get: 92 http://deb.debian.org/debian buster/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 93 http://deb.debian.org/debian buster/main armhf shared-mime-info armhf 1.10-1 [763 kB] Get: 94 http://deb.debian.org/debian buster/main armhf libgdk-pixbuf2.0-common all 2.38.1+dfsg-1 [316 kB] Get: 95 http://deb.debian.org/debian buster/main armhf libgdk-pixbuf2.0-0 armhf 2.38.1+dfsg-1 [161 kB] Get: 96 http://deb.debian.org/debian buster/main armhf gtk-update-icon-cache armhf 3.24.5-1 [80.4 kB] Get: 97 http://deb.debian.org/debian buster/main armhf libpixman-1-0 armhf 0.36.0-1 [465 kB] Get: 98 http://deb.debian.org/debian buster/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB] Get: 99 http://deb.debian.org/debian buster/main armhf libxcb-shm0 armhf 1.13.1-2 [99.0 kB] Get: 100 http://deb.debian.org/debian buster/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 101 http://deb.debian.org/debian buster/main armhf libcairo2 armhf 1.16.0-4 [616 kB] Get: 102 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 103 http://deb.debian.org/debian buster/main armhf fontconfig armhf 2.13.1-2 [404 kB] Get: 104 http://deb.debian.org/debian buster/main armhf libfribidi0 armhf 1.0.5-3.1+deb10u1 [61.7 kB] Get: 105 http://deb.debian.org/debian buster/main armhf libthai-data all 0.1.28-2 [170 kB] Get: 106 http://deb.debian.org/debian buster/main armhf libdatrie1 armhf 0.2.12-2 [35.8 kB] Get: 107 http://deb.debian.org/debian buster/main armhf libthai0 armhf 0.1.28-2 [50.7 kB] Get: 108 http://deb.debian.org/debian buster/main armhf libpango-1.0-0 armhf 1.42.4-8~deb10u1 [169 kB] Get: 109 http://deb.debian.org/debian buster/main armhf libgraphite2-3 armhf 1.3.13-7 [70.3 kB] Get: 110 http://deb.debian.org/debian buster/main armhf libharfbuzz0b armhf 2.3.1-1 [1151 kB] Get: 111 http://deb.debian.org/debian buster/main armhf libpangoft2-1.0-0 armhf 1.42.4-8~deb10u1 [62.7 kB] Get: 112 http://deb.debian.org/debian buster/main armhf libpangocairo-1.0-0 armhf 1.42.4-8~deb10u1 [52.2 kB] Get: 113 http://deb.debian.org/debian buster/main armhf librsvg2-2 armhf 2.44.10-2.1 [955 kB] Get: 114 http://deb.debian.org/debian buster/main armhf librsvg2-common armhf 2.44.10-2.1 [22.9 kB] Get: 115 http://deb.debian.org/debian buster/main armhf adwaita-icon-theme all 3.30.1-1 [11.7 MB] Get: 116 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 117 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 118 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 119 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 120 http://deb.debian.org/debian buster/main armhf binfmt-support armhf 2.2.0-2 [59.3 kB] Get: 121 http://deb.debian.org/debian buster/main armhf libbison-dev armhf 2:3.3.2.dfsg-1 [500 kB] Get: 122 http://deb.debian.org/debian buster/main armhf bison armhf 2:3.3.2.dfsg-1 [848 kB] Get: 123 http://deb.debian.org/debian buster/main armhf openssl armhf 1.1.1d-0+deb10u3 [818 kB] Get: 124 http://deb.debian.org/debian buster/main armhf ca-certificates all 20190110 [157 kB] Get: 125 http://deb.debian.org/debian buster/main armhf libedit2 armhf 3.1-20181209-1 [79.5 kB] Get: 126 http://deb.debian.org/debian buster/main armhf libllvm7 armhf 1:7.0.1-8 [11.3 MB] Get: 127 http://deb.debian.org/debian buster/main armhf libgc1c2 armhf 1:7.6.4-0.4 [212 kB] Get: 128 http://deb.debian.org/debian buster/main armhf libobjc4 armhf 8.3.0-6 [42.2 kB] Get: 129 http://deb.debian.org/debian buster/main armhf libobjc-8-dev armhf 8.3.0-6 [210 kB] Get: 130 http://deb.debian.org/debian buster/main armhf libclang-common-7-dev armhf 1:7.0.1-8 [1357 kB] Get: 131 http://deb.debian.org/debian buster/main armhf libclang1-7 armhf 1:7.0.1-8 [4986 kB] Get: 132 http://deb.debian.org/debian buster/main armhf clang-7 armhf 1:7.0.1-8 [6715 kB] Get: 133 http://deb.debian.org/debian buster/main armhf cmake-data all 3.13.4-1 [1476 kB] Get: 134 http://deb.debian.org/debian buster/main armhf libarchive13 armhf 3.3.3-4+deb10u1 [277 kB] Get: 135 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 136 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 137 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 138 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 139 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 140 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 141 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 142 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 143 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 144 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 145 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 146 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 147 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 148 http://deb.debian.org/debian buster/main armhf libcurl4 armhf 7.64.0-4+deb10u1 [297 kB] Get: 149 http://deb.debian.org/debian buster/main armhf libjsoncpp1 armhf 1.7.4-3 [67.8 kB] Get: 150 http://deb.debian.org/debian buster/main armhf librhash0 armhf 1.3.8-1 [134 kB] Get: 151 http://deb.debian.org/debian buster/main armhf libuv1 armhf 1.24.1-1 [98.0 kB] Get: 152 http://deb.debian.org/debian buster/main armhf cmake armhf 3.13.4-1 [2848 kB] Get: 153 http://deb.debian.org/debian buster/main armhf dbus-user-session armhf 1.12.16-1 [93.4 kB] Get: 154 http://deb.debian.org/debian buster/main armhf libdconf1 armhf 0.30.1-2 [36.4 kB] Get: 155 http://deb.debian.org/debian buster/main armhf dconf-service armhf 0.30.1-2 [31.9 kB] Get: 156 http://deb.debian.org/debian buster/main armhf dconf-gsettings-backend armhf 0.30.1-2 [24.8 kB] Get: 157 http://deb.debian.org/debian buster/main armhf dctrl-tools armhf 2.24-3 [96.0 kB] Get: 158 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 159 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 160 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 161 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 162 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 163 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 164 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 165 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 166 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 167 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 168 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 169 http://deb.debian.org/debian buster/main armhf python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 170 http://deb.debian.org/debian buster/main armhf python3-distutils all 3.7.3-1 [142 kB] Get: 171 http://deb.debian.org/debian buster/main armhf dh-python all 3.20190308 [99.3 kB] Get: 172 http://deb.debian.org/debian buster/main armhf distro-info-data all 0.41+deb10u2 [6584 B] Get: 173 http://deb.debian.org/debian buster/main armhf xml-core all 0.18+nmu1 [23.8 kB] Get: 174 http://deb.debian.org/debian buster/main armhf docutils-common all 0.14+dfsg-4 [167 kB] Get: 175 http://deb.debian.org/debian buster/main armhf libllvm6.0 armhf 1:6.0.1-10 [13.1 MB] Get: 176 http://deb.debian.org/debian buster/main armhf libclang1-6.0 armhf 1:6.0.1-10 [6029 kB] Get: 177 http://deb.debian.org/debian buster/main armhf doxygen armhf 1.8.13-10 [3568 kB] Get: 178 http://deb.debian.org/debian buster/main armhf fonts-lmodern all 2.004.5-6 [4539 kB] Get: 179 http://deb.debian.org/debian buster/main armhf libproxy1v5 armhf 0.4.15-5 [51.0 kB] Get: 180 http://deb.debian.org/debian buster/main armhf glib-networking-common all 2.58.0-2 [59.3 kB] Get: 181 http://deb.debian.org/debian buster/main armhf glib-networking-services armhf 2.58.0-2 [12.8 kB] Get: 182 http://deb.debian.org/debian buster/main armhf gsettings-desktop-schemas all 3.28.1-1 [529 kB] Get: 183 http://deb.debian.org/debian buster/main armhf glib-networking armhf 2.58.0-2 [48.2 kB] Get: 184 http://deb.debian.org/debian buster/main armhf icu-devtools armhf 63.1-6+deb10u1 [168 kB] Get: 185 http://deb.debian.org/debian buster/main armhf imagemagick-6.q16 armhf 8:6.9.10.23+dfsg-2.1 [580 kB] Get: 186 http://deb.debian.org/debian buster/main armhf imagemagick armhf 8:6.9.10.23+dfsg-2.1 [156 kB] Get: 187 http://deb.debian.org/debian buster/main armhf libpaper1 armhf 1.1.28 [20.5 kB] Get: 188 http://deb.debian.org/debian buster/main armhf libpaper-utils armhf 1.1.28 [17.6 kB] Get: 189 http://deb.debian.org/debian buster/main armhf libkpathsea6 armhf 2018.20181218.49446-1 [157 kB] Get: 190 http://deb.debian.org/debian buster/main armhf libptexenc1 armhf 2018.20181218.49446-1 [58.1 kB] Get: 191 http://deb.debian.org/debian buster/main armhf libsynctex2 armhf 2018.20181218.49446-1 [67.4 kB] Get: 192 http://deb.debian.org/debian buster/main armhf libtexlua52 armhf 2018.20181218.49446-1 [86.7 kB] Get: 193 http://deb.debian.org/debian buster/main armhf libtexlua53 armhf 2018.20181218.49446-1 [97.8 kB] Get: 194 http://deb.debian.org/debian buster/main armhf libtexluajit2 armhf 2018.20181218.49446-1 [201 kB] Get: 195 http://deb.debian.org/debian buster/main armhf t1utils armhf 1.41-3 [54.4 kB] Get: 196 http://deb.debian.org/debian buster/main armhf libbrotli1 armhf 1.0.7-2 [259 kB] Get: 197 http://deb.debian.org/debian buster/main armhf libgs9-common all 9.27~dfsg-2+deb10u3 [5136 kB] Get: 198 http://deb.debian.org/debian buster/main armhf libavahi-common-data armhf 0.7-4+b1 [122 kB] Get: 199 http://deb.debian.org/debian buster/main armhf libavahi-common3 armhf 0.7-4+b1 [51.1 kB] Get: 200 http://deb.debian.org/debian buster/main armhf libavahi-client3 armhf 0.7-4+b1 [54.5 kB] Get: 201 http://deb.debian.org/debian buster/main armhf libcups2 armhf 2.2.10-6+deb10u3 [291 kB] Get: 202 http://deb.debian.org/debian buster/main armhf libcupsimage2 armhf 2.2.10-6+deb10u3 [130 kB] Get: 203 http://deb.debian.org/debian buster/main armhf libijs-0.35 armhf 0.35-14 [16.7 kB] Get: 204 http://deb.debian.org/debian buster/main armhf libjbig2dec0 armhf 0.16-1 [54.5 kB] Get: 205 http://deb.debian.org/debian buster/main armhf libgs9 armhf 9.27~dfsg-2+deb10u3 [1900 kB] Get: 206 http://deb.debian.org/debian buster/main armhf libharfbuzz-icu0 armhf 2.3.1-1 [833 kB] Get: 207 http://deb.debian.org/debian buster/main armhf x11-common all 1:7.7+19 [251 kB] Get: 208 http://deb.debian.org/debian buster/main armhf libice6 armhf 2:1.0.9-2 [51.7 kB] Get: 209 http://deb.debian.org/debian buster/main armhf libpotrace0 armhf 1.15-1 [23.9 kB] Get: 210 http://deb.debian.org/debian buster/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 211 http://deb.debian.org/debian buster/main armhf libteckit0 armhf 2.5.8+ds2-5 [246 kB] Get: 212 http://deb.debian.org/debian buster/main armhf libwoff1 armhf 1.0.2-1 [35.8 kB] Get: 213 http://deb.debian.org/debian buster/main armhf libxt6 armhf 1:1.1.5-1+b3 [159 kB] Get: 214 http://deb.debian.org/debian buster/main armhf libxmu6 armhf 2:1.1.2-2+b3 [52.7 kB] Get: 215 http://deb.debian.org/debian buster/main armhf libxpm4 armhf 1:3.5.12-1 [44.0 kB] Get: 216 http://deb.debian.org/debian buster/main armhf libxaw7 armhf 2:1.0.13-1+b2 [167 kB] Get: 217 http://deb.debian.org/debian buster/main armhf libxi6 armhf 2:1.7.9-1 [78.4 kB] Get: 218 http://deb.debian.org/debian buster/main armhf libxxhash0 armhf 0.6.5-2 [10.2 kB] Get: 219 http://deb.debian.org/debian buster/main armhf libzzip-0-13 armhf 0.13.62-3.2 [51.6 kB] Get: 220 http://deb.debian.org/debian buster/main armhf texlive-binaries armhf 2018.20181218.49446-1 [8656 kB] Get: 221 http://deb.debian.org/debian buster/main armhf xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 222 http://deb.debian.org/debian buster/main armhf texlive-base all 2018.20190227-2 [19.7 MB] Get: 223 http://deb.debian.org/debian buster/main armhf texlive-latex-base all 2018.20190227-2 [984 kB] Get: 224 http://deb.debian.org/debian buster/main armhf latexmk all 1:4.61-0.1 [390 kB] Get: 225 http://deb.debian.org/debian buster/main armhf libatk1.0-data all 2.30.0-2 [145 kB] Get: 226 http://deb.debian.org/debian buster/main armhf libatk1.0-0 armhf 2.30.0-2 [43.6 kB] Get: 227 http://deb.debian.org/debian buster/main armhf libatspi2.0-0 armhf 2.30.0-7 [54.8 kB] Get: 228 http://deb.debian.org/debian buster/main armhf libatk-bridge2.0-0 armhf 2.30.0-5 [52.5 kB] Get: 229 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 230 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 231 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 232 http://deb.debian.org/debian buster/main armhf libboost-atomic1.67.0 armhf 1.67.0-13+deb10u1 [226 kB] Get: 233 http://deb.debian.org/debian buster/main armhf libboost-atomic1.67-dev armhf 1.67.0-13+deb10u1 [225 kB] Get: 234 http://deb.debian.org/debian buster/main armhf libboost-chrono1.67.0 armhf 1.67.0-13+deb10u1 [231 kB] Get: 235 http://deb.debian.org/debian buster/main armhf libboost-chrono1.67-dev armhf 1.67.0-13+deb10u1 [234 kB] Get: 236 http://deb.debian.org/debian buster/main armhf libboost-date-time1.67.0 armhf 1.67.0-13+deb10u1 [236 kB] Get: 237 http://deb.debian.org/debian buster/main armhf libboost-serialization1.67.0 armhf 1.67.0-13+deb10u1 [303 kB] Get: 238 http://deb.debian.org/debian buster/main armhf libboost-serialization1.67-dev armhf 1.67.0-13+deb10u1 [370 kB] Get: 239 http://deb.debian.org/debian buster/main armhf libboost-date-time1.67-dev armhf 1.67.0-13+deb10u1 [248 kB] Get: 240 http://deb.debian.org/debian buster/main armhf libboost-dev armhf 1.67.0.1 [3860 B] Get: 241 http://deb.debian.org/debian buster/main armhf libboost-python1.67.0 armhf 1.67.0-13+deb10u1 [307 kB] Get: 242 http://deb.debian.org/debian buster/main armhf libpython2.7 armhf 2.7.16-2+deb10u1 [892 kB] Get: 243 http://deb.debian.org/debian buster/main armhf libexpat1-dev armhf 2.2.6-2+deb10u1 [126 kB] Get: 244 http://deb.debian.org/debian buster/main armhf libpython2.7-dev armhf 2.7.16-2+deb10u1 [31.0 MB] Get: 245 http://deb.debian.org/debian buster/main armhf libpython2-dev armhf 2.7.16-1 [20.9 kB] Get: 246 http://deb.debian.org/debian buster/main armhf libpython-dev armhf 2.7.16-1 [20.9 kB] Get: 247 http://deb.debian.org/debian buster/main armhf python2.7-dev armhf 2.7.16-2+deb10u1 [291 kB] Get: 248 http://deb.debian.org/debian buster/main armhf python2-dev armhf 2.7.16-1 [1216 B] Get: 249 http://deb.debian.org/debian buster/main armhf python-dev armhf 2.7.16-1 [1192 B] Get: 250 http://deb.debian.org/debian buster/main armhf libpython3.7 armhf 3.7.3-2+deb10u1 [1282 kB] Get: 251 http://deb.debian.org/debian buster/main armhf libpython3.7-dev armhf 3.7.3-2+deb10u1 [47.2 MB] Get: 252 http://deb.debian.org/debian buster/main armhf libpython3-dev armhf 3.7.3-1 [20.1 kB] Get: 253 http://deb.debian.org/debian buster/main armhf python3.7-dev armhf 3.7.3-2+deb10u1 [509 kB] Get: 254 http://deb.debian.org/debian buster/main armhf python3-dev armhf 3.7.3-1 [1264 B] Get: 255 http://deb.debian.org/debian buster/main armhf libboost-python1.67-dev armhf 1.67.0-13+deb10u1 [325 kB] Get: 256 http://deb.debian.org/debian buster/main armhf libboost-python-dev armhf 1.67.0.1 [3948 B] Get: 257 http://deb.debian.org/debian buster/main armhf libboost-regex1.67.0 armhf 1.67.0-13+deb10u1 [438 kB] Get: 258 http://deb.debian.org/debian buster/main armhf libicu-dev armhf 63.1-6+deb10u1 [8940 kB] Get: 259 http://deb.debian.org/debian buster/main armhf libboost-regex1.67-dev armhf 1.67.0-13+deb10u1 [538 kB] Get: 260 http://deb.debian.org/debian buster/main armhf libboost-regex-dev armhf 1.67.0.1 [3916 B] Get: 261 http://deb.debian.org/debian buster/main armhf libboost-system1.67-dev armhf 1.67.0-13+deb10u1 [232 kB] Get: 262 http://deb.debian.org/debian buster/main armhf libboost-system-dev armhf 1.67.0.1 [3788 B] Get: 263 http://deb.debian.org/debian buster/main armhf libboost-thread1.67.0 armhf 1.67.0-13+deb10u1 [261 kB] Get: 264 http://deb.debian.org/debian buster/main armhf libboost-thread1.67-dev armhf 1.67.0-13+deb10u1 [270 kB] Get: 265 http://deb.debian.org/debian buster/main armhf libboost-thread-dev armhf 1.67.0.1 [3672 B] Get: 266 http://deb.debian.org/debian buster/main armhf libcairo-gobject2 armhf 1.16.0-4 [123 kB] Get: 267 http://deb.debian.org/debian buster/main armhf libcolord2 armhf 1.4.3-4 [122 kB] Get: 268 http://deb.debian.org/debian buster/main armhf libepoxy0 armhf 1.5.3-0.1 [168 kB] Get: 269 http://deb.debian.org/debian buster/main armhf libffi-dev armhf 3.2.1-9 [154 kB] Get: 270 http://deb.debian.org/debian buster/main armhf libjson-glib-1.0-common all 1.4.4-2 [52.3 kB] Get: 271 http://deb.debian.org/debian buster/main armhf libjson-glib-1.0-0 armhf 1.4.4-2 [53.5 kB] Get: 272 http://deb.debian.org/debian buster/main armhf libsoup2.4-1 armhf 2.64.2-2 [221 kB] Get: 273 http://deb.debian.org/debian buster/main armhf libsoup-gnome2.4-1 armhf 2.64.2-2 [17.5 kB] Get: 274 http://deb.debian.org/debian buster/main armhf librest-0.7-0 armhf 0.8.1-1 [28.5 kB] Get: 275 http://deb.debian.org/debian buster/main armhf libwayland-client0 armhf 1.16.0-1 [21.6 kB] Get: 276 http://deb.debian.org/debian buster/main armhf libwayland-cursor0 armhf 1.16.0-1 [13.0 kB] Get: 277 http://deb.debian.org/debian buster/main armhf libwayland-egl1 armhf 1.16.0-1 [7980 B] Get: 278 http://deb.debian.org/debian buster/main armhf libxcomposite1 armhf 1:0.4.4-2 [16.0 kB] Get: 279 http://deb.debian.org/debian buster/main armhf libxfixes3 armhf 1:5.0.3-1 [20.6 kB] Get: 280 http://deb.debian.org/debian buster/main armhf libxcursor1 armhf 1:1.1.15-2 [33.5 kB] Get: 281 http://deb.debian.org/debian buster/main armhf libxdamage1 armhf 1:1.1.4-3+b3 [14.2 kB] Get: 282 http://deb.debian.org/debian buster/main armhf libxinerama1 armhf 2:1.1.4-2 [17.3 kB] Get: 283 http://deb.debian.org/debian buster/main armhf xkb-data all 2.26-2 [681 kB] Get: 284 http://deb.debian.org/debian buster/main armhf libxkbcommon0 armhf 0.8.2-1 [111 kB] Get: 285 http://deb.debian.org/debian buster/main armhf libxrandr2 armhf 2:1.5.1-1 [34.9 kB] Get: 286 http://deb.debian.org/debian buster/main armhf libgtk-3-common all 3.24.5-1 [3678 kB] Get: 287 http://deb.debian.org/debian buster/main armhf libgtk-3-0 armhf 3.24.5-1 [2198 kB] Get: 288 http://deb.debian.org/debian buster/main armhf libimagequant0 armhf 2.12.2-1.1 [27.2 kB] Get: 289 http://deb.debian.org/debian buster/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get: 290 http://deb.debian.org/debian buster/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB] Get: 291 http://deb.debian.org/debian buster/main armhf libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get: 292 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 293 http://deb.debian.org/debian buster/main armhf liblua5.1-0 armhf 5.1.5-8.1+b2 [86.8 kB] Get: 294 http://deb.debian.org/debian buster/main armhf libncurses-dev armhf 6.1+20181013-2+deb10u2 [295 kB] Get: 295 http://deb.debian.org/debian buster/main armhf libpq5 armhf 11.7-0+deb10u1 [152 kB] Get: 296 http://deb.debian.org/debian buster/main armhf libpq-dev armhf 11.7-0+deb10u1 [150 kB] Get: 297 http://deb.debian.org/debian buster/main armhf librsvg2-bin armhf 2.44.10-2.1 [33.6 kB] Get: 298 http://deb.debian.org/debian buster/main armhf libschroedinger-maeparser1 armhf 1.0.1-4 [37.9 kB] Get: 299 http://deb.debian.org/debian buster/main armhf libschroedinger-coordgenlibs1 armhf 1.1-3 [142 kB] Get: 300 http://deb.debian.org/debian buster/main armhf libschroedinger-coordgenlibs-dev armhf 1.1-3 [27.8 kB] Get: 301 http://deb.debian.org/debian buster/main armhf libschroedinger-maeparser-dev armhf 1.0.1-4 [10.6 kB] Get: 302 http://deb.debian.org/debian buster/main armhf libsqlite3-dev armhf 3.27.2-3 [722 kB] Get: 303 http://deb.debian.org/debian buster/main armhf libtinfo-dev armhf 6.1+20181013-2+deb10u2 [940 B] Get: 304 http://deb.debian.org/debian buster/main armhf libwebpdemux2 armhf 0.6.1-2 [86.6 kB] Get: 305 http://deb.debian.org/debian buster/main armhf libyaml-0-2 armhf 0.2.1-1 [40.6 kB] Get: 306 http://deb.debian.org/debian buster/main armhf llvm-7-runtime armhf 1:7.0.1-8 [162 kB] Get: 307 http://deb.debian.org/debian buster/main armhf llvm-7 armhf 1:7.0.1-8 [3781 kB] Get: 308 http://deb.debian.org/debian buster/main armhf llvm-7-dev armhf 1:7.0.1-8 [20.7 MB] Get: 309 http://deb.debian.org/debian buster/main armhf lsb-release all 10.2019051400 [27.5 kB] Get: 310 http://deb.debian.org/debian buster/main armhf pandoc-data all 2.2.1-3 [329 kB] Get: 311 http://deb.debian.org/debian buster/main armhf pandoc armhf 2.2.1-3+b2 [17.5 MB] Get: 312 http://deb.debian.org/debian buster/main armhf postgresql-client-common all 200+deb10u3 [84.9 kB] Get: 313 http://deb.debian.org/debian buster/main armhf ssl-cert all 1.0.39 [20.8 kB] Get: 314 http://deb.debian.org/debian buster/main armhf postgresql-common all 200+deb10u3 [225 kB] Get: 315 http://deb.debian.org/debian buster/main armhf postgresql-server-dev-11 armhf 11.7-0+deb10u1 [924 kB] Get: 316 http://deb.debian.org/debian buster/main armhf postgresql-server-dev-all all 200+deb10u3 [74.2 kB] Get: 317 http://deb.debian.org/debian buster/main armhf preview-latex-style all 11.91-2 [201 kB] Get: 318 http://deb.debian.org/debian buster/main armhf python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB] Get: 319 http://deb.debian.org/debian buster/main armhf python-six all 1.12.0-1 [15.7 kB] Get: 320 http://deb.debian.org/debian buster/main armhf python-dateutil all 2.7.3-3 [76.8 kB] Get: 321 http://deb.debian.org/debian buster/main armhf python-pkg-resources all 40.8.0-1 [182 kB] Get: 322 http://deb.debian.org/debian buster/main armhf python-numpy armhf 1:1.16.2-1 [1885 kB] Get: 323 http://deb.debian.org/debian buster/main armhf python-tz all 2019.1-1 [33.6 kB] Get: 324 http://deb.debian.org/debian buster/main armhf python-pandas-lib armhf 0.23.3+dfsg-3 [3055 kB] Get: 325 http://deb.debian.org/debian buster/main armhf python-pandas all 0.23.3+dfsg-3 [1750 kB] Get: 326 http://deb.debian.org/debian buster/main armhf python-pil armhf 5.4.1-2+deb10u1 [367 kB] Get: 327 http://deb.debian.org/debian buster/main armhf python3-alabaster all 0.7.8-1 [18.4 kB] Get: 328 http://deb.debian.org/debian buster/main armhf python3-pkg-resources all 40.8.0-1 [153 kB] Get: 329 http://deb.debian.org/debian buster/main armhf python3-tz all 2019.1-1 [27.1 kB] Get: 330 http://deb.debian.org/debian buster/main armhf python3-babel all 2.6.0+dfsg.1-1 [96.7 kB] Get: 331 http://deb.debian.org/debian buster/main armhf python3-certifi all 2018.8.24-1 [140 kB] Get: 332 http://deb.debian.org/debian buster/main armhf python3-chardet all 3.0.4-3 [80.5 kB] Get: 333 http://deb.debian.org/debian buster/main armhf python3-commonmark-bkrs all 0.5.4+ds-2 [28.2 kB] Get: 334 http://deb.debian.org/debian buster/main armhf python3-roman all 2.0.0-3 [8768 B] Get: 335 http://deb.debian.org/debian buster/main armhf python3-docutils all 0.14+dfsg-4 [378 kB] Get: 336 http://deb.debian.org/debian buster/main armhf python3-idna all 2.6-1 [34.3 kB] Get: 337 http://deb.debian.org/debian buster/main armhf python3-imagesize all 1.0.0-1 [4960 B] Get: 338 http://deb.debian.org/debian buster/main armhf python3-markupsafe armhf 1.1.0-1 [14.2 kB] Get: 339 http://deb.debian.org/debian buster/main armhf python3-jinja2 all 2.10-2 [106 kB] Get: 340 http://deb.debian.org/debian buster/main armhf python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get: 341 http://deb.debian.org/debian buster/main armhf python3-six all 1.12.0-1 [15.7 kB] Get: 342 http://deb.debian.org/debian buster/main armhf python3-packaging all 19.0-1 [20.5 kB] Get: 343 http://deb.debian.org/debian buster/main armhf python3-pygments all 2.3.1+dfsg-1 [594 kB] Get: 344 http://deb.debian.org/debian buster/main armhf python3-recommonmark all 0.4.0+ds-5 [14.9 kB] Get: 345 http://deb.debian.org/debian buster/main armhf python3-urllib3 all 1.24.1-1 [97.1 kB] Get: 346 http://deb.debian.org/debian buster/main armhf python3-requests all 2.21.0-1 [66.9 kB] Get: 347 http://deb.debian.org/debian buster/main armhf sphinx-common all 1.8.4-1 [500 kB] Get: 348 http://deb.debian.org/debian buster/main armhf python3-sphinx all 1.8.4-1 [481 kB] Get: 349 http://deb.debian.org/debian buster/main armhf rapidjson-dev all 1.1.0+dfsg2-5 [98.7 kB] Get: 350 http://deb.debian.org/debian buster/main armhf texlive-fonts-recommended all 2018.20190227-2 [5228 kB] Get: 351 http://deb.debian.org/debian buster/main armhf texlive-plain-generic all 2018.20190227-2 [24.3 MB] Get: 352 http://deb.debian.org/debian buster/main armhf texlive-generic-extra all 2018.20190227-2 [32.2 kB] Get: 353 http://deb.debian.org/debian buster/main armhf texlive-latex-recommended all 2018.20190227-2 [15.2 MB] Get: 354 http://deb.debian.org/debian buster/main armhf texlive-pictures all 2018.20190227-2 [8201 kB] Get: 355 http://deb.debian.org/debian buster/main armhf texlive-latex-extra all 2018.20190227-2 [12.3 MB] Fetched 405 MB in 1min 20s (5060 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libapparmor1_2.13.2-10_armhf.deb ... Unpacking libapparmor1:armhf (2.13.2-10) ... Selecting previously unselected package libcap2:armhf. Preparing to unpack .../01-libcap2_1%3a2.25-2_armhf.deb ... Unpacking libcap2:armhf (1:2.25-2) ... Selecting previously unselected package libargon2-1:armhf. 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Selecting previously unselected package libidn11:armhf. Preparing to unpack .../08-libidn11_1.33-2.2_armhf.deb ... Unpacking libidn11:armhf (1.33-2.2) ... Selecting previously unselected package libip4tc0:armhf. Preparing to unpack .../09-libip4tc0_1.8.2-4_armhf.deb ... Unpacking libip4tc0:armhf (1.8.2-4) ... Selecting previously unselected package libkmod2:armhf. Preparing to unpack .../10-libkmod2_26-1_armhf.deb ... Unpacking libkmod2:armhf (26-1) ... Selecting previously unselected package systemd. Preparing to unpack .../11-systemd_241-7~deb10u4_armhf.deb ... Unpacking systemd (241-7~deb10u4) ... Setting up libapparmor1:armhf (2.13.2-10) ... Setting up libcap2:armhf (1:2.25-2) ... Setting up libargon2-1:armhf (0~20171227-0.2) ... Setting up libjson-c3:armhf (0.12.1+ds-2) ... Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libidn11:armhf (1.33-2.2) ... Setting up libip4tc0:armhf (1.8.2-4) ... Setting up libkmod2:armhf (26-1) ... Setting up libdevmapper1.02.1:armhf (2:1.02.155-3) ... Setting up libcryptsetup12:armhf (2:2.1.0-5+deb10u2) ... Setting up systemd (241-7~deb10u4) ... Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service -> /lib/systemd/system/getty@.service. Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target -> /lib/systemd/system/remote-fs.target. Created symlink /etc/systemd/system/dbus-org.freedesktop.timesync1.service -> /lib/systemd/system/systemd-timesyncd.service. Created symlink /etc/systemd/system/sysinit.target.wants/systemd-timesyncd.service -> /lib/systemd/system/systemd-timesyncd.service. Initializing machine ID from random generator. Setting up dmsetup (2:1.02.155-3) ... Selecting previously unselected package systemd-sysv. (Reading database ... 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Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../09-python2-minimal_2.7.16-1_armhf.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../10-python-minimal_2.7.16-1_armhf.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_armhf.deb ... Unpacking libexpat1:armhf (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:armhf. Preparing to unpack .../14-libreadline7_7.0-5_armhf.deb ... Unpacking libreadline7:armhf (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:armhf. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:armhf. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython2-stdlib:armhf (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:armhf. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython-stdlib:armhf (2.7.16-1) ... Setting up libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21254 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_armhf.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Unpacking libpython3.7-minimal:armhf (3.7.3-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../38-python3.7-minimal_3.7.3-2+deb10u1_armhf.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u1) ... Setting up libpython3.7-minimal:armhf (3.7.3-2+deb10u1) ... Setting up libexpat1:armhf (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23128 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_armhf.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:armhf. Preparing to unpack .../libmpdec2_2.4.2-2_armhf.deb ... Unpacking libmpdec2:armhf (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:armhf. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u1_armhf.deb ... Unpacking libpython3.7-stdlib:armhf (3.7.3-2+deb10u1) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u1_armhf.deb ... Unpacking python3.7 (3.7.3-2+deb10u1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../libpython3-stdlib_3.7.3-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23540 files and directories currently installed.) Preparing to unpack .../000-python3_3.7.3-1_armhf.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package tex-common. Preparing to unpack .../002-tex-common_6.11_all.deb ... Unpacking tex-common (6.11) ... 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Setting up libgdk-pixbuf2.0-common (2.38.1+dfsg-1) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up xkb-data (2.26-2) ... Setting up libobjc4:armhf (8.3.0-6) ... Setting up libzzip-0-13:armhf (0.13.62-3.2) ... Setting up libboost-date-time1.67.0:armhf (1.67.0-13+deb10u1) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libffi-dev:armhf (3.2.1-9) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libjbig0:armhf (2.1-3.1+b2) ... Setting up libcolord2:armhf (1.4.3-4) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up python-babel-localedata (2.6.0+dfsg.1-1) ... Setting up rapidjson-dev (1.1.0+dfsg2-5) ... 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Setting up dbus (1.12.16-1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsigsegv2:armhf (2.12-2) ... Setting up libfribidi0:armhf (1.0.5-3.1+deb10u1) ... Setting up t1utils (1.41-3) ... Setting up libimagequant0:armhf (2.12.2-1.1) ... Setting up libpng16-16:armhf (1.6.36-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up binfmt-support (2.2.0-2) ... Created symlink /etc/systemd/system/multi-user.target.wants/binfmt-support.service -> /lib/systemd/system/binfmt-support.service. Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libwebp6:armhf (0.6.1-2) ... Setting up icu-devtools (63.1-6+deb10u1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libltdl7:armhf (2.4.6-9) ... Setting up libfftw3-double3:armhf (3.3.8-2) ... Setting up libkpathsea6:armhf (2018.20181218.49446-1) ... 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Setting up libjson-glib-1.0-0:armhf (1.4.4-2) ... Setting up libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Setting up libthai0:armhf (0.1.28-2) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up dbus-user-session (1.12.16-1) ... Setting up libboost-date-time1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libblas3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up doxygen (1.8.13-10) ... Setting up libptexenc1:armhf (2018.20181218.49446-1) ... Setting up pandoc (2.2.1-3+b2) ... Setting up libfreetype6:armhf (2.9.1-3+deb10u1) ... Setting up ssl-cert (1.0.39) ... Setting up shared-mime-info (1.10-1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libwayland-cursor0:armhf (1.16.0-1) ... Setting up xml-core (0.18+nmu1) ... Setting up bison (2:3.3.2.dfsg-1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libcurl4:armhf (7.64.0-4+deb10u1) ... Setting up libllvm7:armhf (1:7.0.1-8) ... Setting up libx11-6:armhf (2:1.6.7-1) ... Setting up libharfbuzz0b:armhf (2.3.1-1) ... Setting up libclang1-7 (1:7.0.1-8) ... Setting up libboost-regex-dev:armhf (1.67.0.1) ... Setting up libxcomposite1:armhf (1:0.4.4-2) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up libavahi-client3:armhf (0.7-4+b1) ... Setting up libpython3-stdlib:armhf (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libtinfo-dev:armhf (6.1+20181013-2+deb10u2) ... Setting up libpaper1:armhf (1.1.28) ... Creating config file /etc/papersize with new version Setting up python3.7 (3.7.3-2+deb10u1) ... Setting up libpython2.7:armhf (2.7.16-2+deb10u1) ... Setting up flex (2.6.4-6.2) ... Setting up liblapack3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libpython2.7-dev:armhf (2.7.16-2+deb10u1) ... Setting up gettext (0.19.8.1-9) ... Setting up libharfbuzz-icu0:armhf (2.3.1-1) ... Setting up libpython3-dev:armhf (3.7.3-1) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up llvm-7-runtime (1:7.0.1-8) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up llvm-7 (1:7.0.1-8) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libschroedinger-coordgenlibs-dev:armhf (1.1-3) ... Setting up libboost-thread1.67-dev:armhf (1.67.0-13+deb10u1) ... Setting up libpython2-stdlib:armhf (2.7.16-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libpq5:armhf (11.7-0+deb10u1) ... Setting up libxext6:armhf (2:1.3.3-1+b2) ... Setting up libpq-dev (11.7-0+deb10u1) ... Setting up dconf-service (0.30.1-2) ... Setting up python3 (3.7.3-1) ... Setting up libpaper-utils (1.1.28) ... Setting up libatspi2.0-0:armhf (2.30.0-7) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer. Setting up python3-markupsafe (1.1.0-1) ... Setting up python2 (2.7.16-1) ... Setting up python3.7-dev (3.7.3-2+deb10u1) ... Setting up python3-tz (2019.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up tex-common (6.11) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libatk-bridge2.0-0:armhf (2.30.0-5) ... Setting up libpython-stdlib:armhf (2.7.16-1) ... Setting up python3-roman (2.0.0-3) ... Setting up python3-jinja2 (2.10-2) ... Setting up python3-pygments (2.3.1+dfsg-1) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-certifi (2018.8.24-1) ... Setting up libxfixes3:armhf (1:5.0.3-1) ... Setting up libgdk-pixbuf2.0-0:armhf (2.38.1+dfsg-1) ... Setting up sphinx-common (1.8.4-1) ... Setting up libxinerama1:armhf (2:1.1.4-2) ... Setting up postgresql-common (200+deb10u3) ... Adding user postgres to group ssl-cert Creating config file /etc/postgresql-common/createcluster.conf with new version Building PostgreSQL dictionaries from installed myspell/hunspell packages... Removing obsolete dictionary files: Created symlink /etc/systemd/system/multi-user.target.wants/postgresql.service -> /lib/systemd/system/postgresql.service. Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up python3-idna (2.6-1) ... Setting up libxrandr2:armhf (2:1.5.1-1) ... Setting up libxt6:armhf (1:1.1.5-1+b3) ... Setting up python3-urllib3 (1.24.1-1) ... Setting up libcups2:armhf (2.2.10-6+deb10u3) ... Setting up python3-commonmark-bkrs (0.5.4+ds-2) ... Setting up libclang-common-7-dev (1:7.0.1-8) ... Setting up cmake (3.13.4-1) ... Setting up libpython2-dev:armhf (2.7.16-1) ... Setting up libfontconfig1:armhf (2.13.1-2) ... Setting up lsb-release (10.2019051400) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up libboost-thread-dev:armhf (1.67.0.1) ... Setting up python3-imagesize (1.0.0-1) ... Setting up python2.7-dev (2.7.16-2+deb10u1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up clang-7 (1:7.0.1-8) ... Setting up llvm-7-dev (1:7.0.1-8) ... Setting up gtk-update-icon-cache (3.24.5-1) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxmu6:armhf (2:1.1.2-2+b3) ... Setting up libxdamage1:armhf (1:1.1.4-3+b3) ... Setting up python2-dev (2.7.16-1) ... Setting up libxi6:armhf (2:1.7.9-1) ... Setting up dconf-gsettings-backend:armhf (0.30.1-2) ... Setting up python3-babel (2.6.0+dfsg.1-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python-pkg-resources (40.8.0-1) ... Setting up python3-alabaster (0.7.8-1) ... Setting up po-debconf (1.0.21) ... Setting up preview-latex-style (11.91-2) ... Setting up libxcursor1:armhf (1:1.1.15-2) ... Setting up libpango-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up python-pil:armhf (5.4.1-2+deb10u1) ... Setting up libxaw7:armhf (2:1.0.13-1+b2) ... Setting up libcairo2:armhf (1.16.0-4) ... Setting up libcupsimage2:armhf (2.2.10-6+deb10u3) ... Setting up libpython-dev:armhf (2.7.16-1) ... Setting up python-six (1.12.0-1) ... Setting up libmagickcore-6.q16-6:armhf (8:6.9.10.23+dfsg-2.1) ... Setting up python-dateutil (2.7.3-3) ... Setting up python3-packaging (19.0-1) ... Setting up python3-chardet (3.0.4-3) ... Setting up python3-dev (3.7.3-1) ... Setting up python3-requests (2.21.0-1) ... Setting up postgresql-server-dev-11 (11.7-0+deb10u1) ... Setting up python-tz (2019.1-1) ... Setting up libmagickwand-6.q16-6:armhf (8:6.9.10.23+dfsg-2.1) ... Setting up libcairo-gobject2:armhf (1.16.0-4) ... Setting up libpangoft2-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up postgresql-server-dev-all (200+deb10u3) ... Setting up libgtk-3-common (3.24.5-1) ... Setting up libpangocairo-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up python-dev (2.7.16-1) ... Setting up gsettings-desktop-schemas (3.28.1-1) ... Setting up libgs9:armhf (9.27~dfsg-2+deb10u3) ... Setting up python-numpy (1:1.16.2-1) ... Setting up librsvg2-2:armhf (2.44.10-2.1) ... Setting up librsvg2-common:armhf (2.44.10-2.1) ... Setting up imagemagick-6.q16 (8:6.9.10.23+dfsg-2.1) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up texlive-binaries (2018.20181218.49446-1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up glib-networking:armhf (2.58.0-2) ... Setting up libboost-python1.67-dev (1.67.0-13+deb10u1) ... Setting up python-pandas-lib (0.23.3+dfsg-3) ... Setting up texlive-base (2018.20190227-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex Setting up libsoup2.4-1:armhf (2.64.2-2) ... Setting up texlive-plain-generic (2018.20190227-2) ... Setting up python-pandas (0.23.3+dfsg-3) ... Setting up libboost-python-dev (1.67.0.1) ... Setting up texlive-latex-base (2018.20190227-2) ... Setting up adwaita-icon-theme (3.30.1-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up texlive-latex-recommended (2018.20190227-2) ... Setting up texlive-pictures (2018.20190227-2) ... Setting up imagemagick (8:6.9.10.23+dfsg-2.1) ... Setting up texlive-fonts-recommended (2018.20190227-2) ... Setting up libsoup-gnome2.4-1:armhf (2.64.2-2) ... Setting up librest-0.7-0:armhf (0.8.1-1) ... Setting up texlive-generic-extra (2018.20190227-2) ... Setting up libgtk-3-0:armhf (3.24.5-1) ... Setting up latexmk (1:4.61-0.1) ... Setting up texlive-latex-extra (2018.20190227-2) ... Setting up librsvg2-bin (2.44.10-2.1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for systemd (241-7~deb10u4) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-4) ... Processing triggers for sgml-base (1.29) ... Setting up python3-docutils (0.14+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-recommonmark (0.4.0+ds-5) ... Setting up python3-sphinx (1.8.4-1) ... update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for libgdk-pixbuf2.0-0:armhf (2.38.1+dfsg-1) ... Processing triggers for tex-common (6.11) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/rdkit-201809.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 201809.1+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael Banck dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean pg_buildext checkcontrol dh clean --with python2 --buildsystem=cmake --parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/rdkit-201809.1+dfsg' find /build/rdkit-201809.1+dfsg -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/Cookbook.rst \ Docs/Book/Install.rst \ Docs/Book/Overview.rst \ rdkit/ML/Data/test_data/testgeneral.dat.pkl \ rdkit/ML/Data/test_data/testquant.qdat.pkl rm -f Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps dh_auto_clean pg_buildext clean /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit build-%v ### clean 11 ### make[1]: Leaving directory '/build/rdkit-201809.1+dfsg' dh_clean -O--buildsystem=cmake -O--parallel debian/rules build dh build --with python2 --buildsystem=cmake --parallel dh_update_autotools_config -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/build/rdkit-201809.1+dfsg' 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_OPTIMIZE_NATIVE=OFF cd obj-arm-linux-gnueabihf && 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_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -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_OPTIMIZE_NATIVE=OFF .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- Found Catch2 source in /build/rdkit-201809.1+dfsg/External/catch/catch CATCH: /build/rdkit-201809.1+dfsg/External/catch/catch/single_include -- Found PythonInterp: /usr/bin/python (found version "2.7.16") -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython2.7.so (found version "2.7.16") Python Install directory /usr/lib/python2.7/dist-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") Eigen3 not found, disabling the Descriptors3D build. -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Boost version: 1.67.0 -- Found the following Boost libraries: -- serialization == Using strict rotor definition == Updating Filters.cpp from pains file == Done updating pains files -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/rdkit-201809.1+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/rdkit-201809.1+dfsg' dh_auto_build cd obj-arm-linux-gnueabihf && make -j4 make[2]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/rdkit-201809.1+dfsg -B/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/External/catch /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/catch /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/External/INCHI-API /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= Scanning dependencies of target catch make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build Scanning dependencies of target inchi_support make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[4]: Nothing to be done for 'External/catch/CMakeFiles/catch.dir/build'. make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API && /usr/bin/cmake -E copy /build/rdkit-201809.1+dfsg/External/INCHI-API/python/noinchi.py /build/rdkit-201809.1+dfsg/rdkit/Chem/inchi.py [ 0%] Built target catch make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/Cluster/Murtagh /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= [ 0%] Built target inchi_support Scanning dependencies of target RDGeneral make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target hc make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o [ 2%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.cpp cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cc -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -o CMakeFiles/hc.dir/hc.c.o -c /build/rdkit-201809.1+dfsg/Code/ML/Cluster/Murtagh/hc.c [ 2%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cc -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/rdkit-201809.1+dfsg/Code/ML/Cluster/Murtagh/hcdriver.c [ 2%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2018.09.1 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2018.09.1 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 2%] Built target hc [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeneral.dir/Dict.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.cpp [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/LocaleSwitcher.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/versions.cpp [ 3%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2018.09.1 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/Dict.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 3%] Built target RDGeneral make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDBoost /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target testRDValue make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target RDBoost make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build Scanning dependencies of target testDict make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target DataStructs [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/testRDValue.cpp make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 3%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/c++ -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap.cpp [ 4%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDGeneral/testDict.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/BitVect.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/SparseBitVect.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-taggedunion.h:40, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue.h:39, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 [ 5%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2018.09.1 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2018.09.1 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 5%] Built target RDBoost make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= Scanning dependencies of target testMatrices make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 5%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Numerics/testMatrices.cpp In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-taggedunion.h:40, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue.h:39, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/8/bits/stl_vector.h: In function 'void testVector() [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testDict.cpp:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-taggedunion.h:40, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue.h:39, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-taggedunion.h:40, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue.h:39, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/8/bits/stl_vector.h: In function 'void testVector() [with T = long double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-taggedunion.h:40, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue.h:39, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testRDValue.cpp:2: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/ExplicitBitVect.cpp /usr/include/c++/8/bits/vector.tcc: In function 'void testVectToString()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testDict.cpp:14: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, RDKit::RDAny>; _KeyOfValue = std::_Select1st, RDKit::RDAny> >; _Compare = std::less >; _Alloc = std::allocator, RDKit::RDAny> >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, RDKit::RDAny>, std::_Select1st, RDKit::RDAny> >, std::less >, std::allocator, RDKit::RDAny> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, RDKit::RDAny> >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testDict.cpp:14: /usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = RDKit::RDAny; _Compare = std::less >; _Alloc = std::allocator, RDKit::RDAny> >]': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, RDKit::RDAny>, std::_Select1st, RDKit::RDAny> >, std::less >, std::allocator, RDKit::RDAny> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, RDKit::RDAny> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 5%] Linking CXX executable testRDValue cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 5%] Built target testRDValue make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/EigenSolvers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= Scanning dependencies of target EigenSolvers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/testDict.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'void testRDAny()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 5%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/c++ -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Utils.cpp [ 5%] Linking CXX executable testMatrices cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 5%] Built target testMatrices make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Catalogs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= Scanning dependencies of target Catalogs make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.cpp [ 5%] Linking CXX executable testDict cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/base64.cpp make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 5%] Built target testDict make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Query /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Query /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= Scanning dependencies of target testQuery make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 5%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Query/test.cpp [ 6%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 6%] Built target EigenSolvers make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= Scanning dependencies of target testMatCalc make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 7%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/BitOps.cpp [ 7%] Linking CXX executable testMatCalc cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 7%] Built target testMatCalc make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/SimDivPickers 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-I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/SimDivPickers/DistPicker.cpp [ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Catalogs/CatalogParams.cpp [ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Catalogs/CatalogEntry.cpp [ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2018.09.1 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 7%] Built target Catalogs make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/Cluster/Murtagh /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= Scanning dependencies of target Clustering make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 7%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ML/Cluster/Murtagh/Clustering.cpp [ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/SimDivPickers/MaxMinPicker.cpp [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/DiscreteDistMat.cpp [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/DiscreteValueVect.cpp [ 9%] Linking CXX executable testQuery cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 9%] Built target testQuery make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= Scanning dependencies of target rdBase make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 9%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp [ 9%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 9%] Built target Clustering [ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/FPBReader.cpp [ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.cpp [ 9%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2018.09.1 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2018.09.1 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 9%] Built target SimDivPickers make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/SimDivPickers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target testSimDivPickers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/SimDivPickers/testPickers.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:24, from /usr/include/boost/dynamic_bitset.hpp:15, from /build/rdkit-201809.1+dfsg/Code/DataStructs/ExplicitBitVect.h:16, from /build/rdkit-201809.1+dfsg/Code/DataStructs/FPBReader.cpp:15: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/core/swap.hpp:25, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from /usr/include/boost/tuple/tuple_comparison.hpp:19, from /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.cpp:11: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /usr/include/boost/core/swap.hpp:25, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from /usr/include/boost/tuple/tuple_comparison.hpp:19, from /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.cpp:11: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = boost::tuples::tuple; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/core/swap.hpp:25, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from /usr/include/boost/tuple/tuple_comparison.hpp:19, from /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.cpp:11: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Ranking.h:21, from /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.cpp:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {boost::tuples::tuple}; _Tp = boost::tuples::tuple; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {boost::tuples::tuple}; _Tp = boost::tuples::tuple; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = boost::tuples::tuple; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Ranking.h:21, from /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::{anonymous}::generic_nbr_helper(std::vector >&, T, const RDKit::{anonymous}::sim_args&, unsigned int) [with T = void (*)(unsigned int, unsigned int, const RDKit::{anonymous}::sim_args*)]': /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/core/swap.hpp:25, from /usr/include/boost/utility/swap.hpp:15, from /usr/include/boost/tuple/detail/tuple_basic.hpp:40, from /usr/include/boost/tuple/tuple.hpp:28, from /usr/include/boost/tuple/tuple_comparison.hpp:19, from /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.cpp:11: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 10%] Linking CXX executable testSimDivPickers cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread ../../lib/libRDKithc.so.1.2018.09.1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 10%] Built target testSimDivPickers In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:23, from /usr/include/boost/dynamic_bitset.hpp:15, from /build/rdkit-201809.1+dfsg/Code/DataStructs/ExplicitBitVect.h:16, from /build/rdkit-201809.1+dfsg/Code/DataStructs/FPBReader.cpp:15: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:23, from /usr/include/boost/dynamic_bitset.hpp:15, from /build/rdkit-201809.1+dfsg/Code/DataStructs/ExplicitBitVect.h:16, from /build/rdkit-201809.1+dfsg/Code/DataStructs/FPBReader.cpp:15: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:23, from /usr/include/boost/dynamic_bitset.hpp:15, from /build/rdkit-201809.1+dfsg/Code/DataStructs/ExplicitBitVect.h:16, from /build/rdkit-201809.1+dfsg/Code/DataStructs/FPBReader.cpp:15: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'std::vector > RDKit::FPBReader::getTverskyNeighbors(const uint8_t*, double, double, double, bool) const': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'std::vector > RDKit::FPBReader::getTanimotoNeighbors(const uint8_t*, double, bool) const': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 10%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2018.09.1 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 10%] Built target DataStructs make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= Scanning dependencies of target testFPB Scanning dependencies of target testMultiFPB make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target testDataStructs make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 10%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/testMultiFPB.cpp [ 11%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/testFPB.cpp [ 12%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/testDatastructs.cpp In file included from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:15: /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:185:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:155:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ [ 12%] Linking CXX executable testFPB cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 12%] Built target testFPB make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target cDataStructs make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/DataStructs.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void boost::python::container_utils::extend_container(Container&, boost::python::api::object) [with Container = std::vector]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 14%] Linking CXX executable testMultiFPB cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 14%] Built target testMultiFPB make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= Scanning dependencies of target RDGeometryLib make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/point.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = double; Index = unsigned int; Key = double]': /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/function/detail/prologue.hpp:13, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In static member function 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = double; Index = unsigned int; Key = double]': /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1266:2: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 insert(const_iterator __position, _InputIterator __first, ^~~~~~ /usr/include/c++/8/bits/stl_vector.h:1266:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1266:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = double; Index = unsigned int]': /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/vector.tcc:149:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(begin() + (__position - cbegin()), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/vector.tcc:149:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(begin() + (__position - cbegin()), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:5, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:113:17: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 container.insert(container.begin()+from, first, last); ^~~~~~~~~ /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:113:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ In file included from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:5, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:117:17: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 container.insert(container.begin()+from, first, last); ^~~~~~~~~ /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:117:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap/RDBase.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void boost::python::vector_indexing_suite::base_extend(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]': /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/Transform2D.cpp [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 14%] Linking CXX executable testDataStructs cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 14%] Built target testDataStructs make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= Scanning dependencies of target rdMetricMatrixCalc make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 14%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/Transform3D.cpp [ 14%] Linking CXX shared module ../../../rdkit/rdBase.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/UniformGrid3D.cpp [ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/SparseIntVect.cpp make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 14%] Built target rdBase make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/SimDivPickers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target rdSimDivPickers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/SimDivPickers/Wrap/MaxMinPicker.cpp In file included from /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'double RDDataManip::EuclideanDistanceMetric(const T1&, const T2&, unsigned int) [with T1 = PySequenceHolder; T2 = PySequenceHolder]': /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 14%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 14%] Built target rdMetricMatrixCalc make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= Scanning dependencies of target InfoTheory make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 14%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/c++ -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoBitRanker.cpp [ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/GridUtils.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoBitRanker.h:15, from /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoBitRanker.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoBitRanker.h:15, from /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoBitRanker.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In member function 'double* RDInfoTheory::InfoBitRanker::getTopN(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 15%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2018.09.1 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2018.09.1 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 15%] Built target InfoTheory make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= Scanning dependencies of target rdInfoTheory make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 15%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Geometry/GridUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/Geometry/GridUtils.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/SimDivPickers/Wrap/MaxMinPicker.cpp: In member function 'RDKit::INT_VECT RDPickers::MaxMinPicker::lazyPick(T&, unsigned int, unsigned int, const INT_VECT&, int, double&) const [with T = RDPickers::pyobjFunctor]': /build/rdkit-201809.1+dfsg/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:63:48: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] return python::extract(dp_obj(i, j)); ^ /build/rdkit-201809.1+dfsg/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:63:48: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] return python::extract(dp_obj(i, j)); ^ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Geometry/GridUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/Geometry/GridUtils.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector RDGeom::findGridTerminalPoints(const RDGeom::UniformGrid3D&, double, double)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 16%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 16%] Built target RDGeometryLib make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/Data /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= Scanning dependencies of target cQuantize make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 16%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ML/Data/cQuantize.cpp [ 16%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp In file included from /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/SparseIntVect.cpp:18: /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = long long int]': /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 16%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so [ 16%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 16%] Built target cQuantize make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target ChemicalFeatures make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 16%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/FreeChemicalFeature.cpp /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'void {anonymous}::pyUpdateFromSequence(RDKit::SparseIntVect&, boost::python::api::object&) [with IndexType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 16%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp [ 16%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2018.09.1 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2018.09.1 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 16%] Built target ChemicalFeatures make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testTransforms make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 16%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/testTransforms.cpp [ 17%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2018.09.1 ../../../lib/libRDKithc.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 17%] Built target rdSimDivPickers [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/wrap_SparseBV.cpp [ 17%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp [ 18%] Linking CXX executable testTransforms cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 18%] Built target testTransforms make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= Scanning dependencies of target testGrid make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 18%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/testGrid.cpp [ 18%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -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.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 18%] Built target rdInfoTheory make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Geometry/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= Scanning dependencies of target rdGeometry make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make 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/build/rdkit-201809.1+dfsg/Code/Geometry/Wrap/Point.cpp [ 18%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/wrap_BitOps.cpp [ 18%] Linking CXX executable testGrid cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 18%] Built target testGrid make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= Scanning dependencies of target Alignment make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 18%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment/AlignPoints.cpp [ 19%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/wrap_FPB.cpp [ 19%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2018.09.1 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 19%] Built target Alignment make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= Scanning dependencies of target GraphMol make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 19%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/Wrap/UniformGrid3D.cpp [ 19%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap/wrap_Utils.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryAtom.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryBond.cpp [ 20%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Bond.cpp make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 20%] Built target cDataStructs make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target testChemicalFeatures make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 20%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/testChemicalFeatures.cpp [ 21%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Geometry/Wrap/rdGeometry.cpp [ 21%] Linking CXX executable testChemicalFeatures cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 21%] Built target testChemicalFeatures make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= Scanning dependencies of target testAlignment make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 21%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment/testAlignment.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FindRings.cpp [ 21%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 21%] Built target rdGeometry make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= Scanning dependencies of target rdAlignment make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 21%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment/Wrap/rdAlignment.cpp [ 21%] Linking CXX executable testAlignment cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 21%] Built target testAlignment [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FindRings.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.cpp In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'std::map > RDKit::MolOps::getMolFragsWithQuery(const RDKit::ROMol&, T (*)(const RDKit::ROMol&, const RDKit::Atom*), bool, const std::vector*, bool) [with T = std::__cxx11::basic_string]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:16: /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'void RDNumeric::Alignments::GetPointsFromPythonSequence(boost::python::api::object&, RDGeom::Point3DConstPtrVect&)': /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ /usr/include/c++/8/bits/stl_vector.h: In function 'std::map > RDKit::MolOps::getMolFragsWithQuery(const RDKit::ROMol&, T (*)(const RDKit::ROMol&, const RDKit::Atom*), bool, const std::vector*, bool) [with T = int]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'std::map > RDKit::MolOps::getMolFragsWithQuery(const RDKit::ROMol&, T (*)(const RDKit::ROMol&, const RDKit::Atom*), bool, const std::vector*, bool) [with T = unsigned int]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/8/bits/vector.tcc: In function 'std::vector > RDKit::MolOps::getMolFrags(const RDKit::ROMol&, bool, RDKit::INT_VECT*, RDKit::VECT_INT_VECT*, bool)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.cpp:11: /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'PyObject* RDNumeric::Alignments::AlignPointPairs(boost::python::api::object, boost::python::api::object, boost::python::api::object, bool, unsigned int)': /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 22%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 22%] Built target rdAlignment [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/PeriodicTable.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/atomic_data.cpp In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'unsigned int RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.h:21, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.h:21, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/PeriodicTable.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/PeriodicTable.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::atomicData&}; _Tp = RDKit::atomicData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.h:21, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/GraphMol/PeriodicTable.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/PeriodicTable.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::PeriodicTable::PeriodicTable()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.h:21, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Canon.cpp /usr/include/c++/8/bits/stl_vector.h: In member function 'unsigned int RDKit::RWMol::addAtom(bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/AtomIterators.cpp [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/BondIterators.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Canon.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Aromaticity.cpp [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Kekulize.cpp [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDiscriminators.cpp In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void RDKit::MolPickler::_addAtomFromPickleV1(std::istream&, RDKit::ROMol*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Aromaticity.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDiscriminators.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ConjugHybrid.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/AddHs.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Matrices.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Chirality.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/RingInfo.cpp [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/AddHs.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/AddHs.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/AddHs.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Matrices.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/AddHs.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::MolOps::removeHs(RDKit::RWMol&, bool, bool, bool)': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::MolOps::addHs(RDKit::RWMol&, bool, bool, const UINT_VECT*, bool)': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Chirality.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 24%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Renumber.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'RDKit::Conformer::Conformer(const RDKit::Conformer&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/AdjustQuery.cpp [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Resonance.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Renumber.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Renumber.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Renumber.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Renumber.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::ROMol* RDKit::MolOps::renumberAtoms(const RDKit::ROMol&, const std::vector&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StereoGroup.cpp [ 25%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/new_canon.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Resonance.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void RDKit::ResonanceUtils::fixExplicitImplicitHs(RDKit::ROMol&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 25%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2018.09.1 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Built target GraphMol make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= Scanning dependencies of target Trajectory make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target MolTransforms make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build Scanning dependencies of target SubstructMatch make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target SmilesParse make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build [ 25%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct/SubstructMatch.cpp [ 25%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/MolTransforms.cpp [ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParse.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:118:5: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:149:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(begin() + (__position - cbegin()), __x); ^~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp: In member function 'unsigned int RDKit::Trajectory::insertSnapshot(unsigned int, RDKit::Snapshot)': /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp:73:74: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 return (d_snapshotVect->insert(d_snapshotVect->begin() + snapshotNum, s) - ^ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.h:21, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParse.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParse.cpp:26: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In member function 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 25%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2018.09.1 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Built target Trajectory make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= Scanning dependencies of target Subgraphs make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/Subgraphs.cpp /usr/include/c++/8/bits/vector.tcc: In function 'RDKit::RWMol* RDKit::SmilesToMol(const string&, const RDKit::SmilesParserParams&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 25%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Built target MolTransforms make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target PartialCharges make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.cpp [ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct/SubstructUtils.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::computeGasteigerCharges(const RDKit::ROMol&, std::vector&, int, bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 26%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.cpp [ 26%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerParams.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 26%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 26%] Built target SubstructMatch make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolTransforms make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 26%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/Subgraphs.h:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/Subgraphs.h:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.cpp /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::ROMol* RDKit::Subgraphs::pathToSubmol(const RDKit::ROMol&, const PATH_TYPE&, bool, RDKit::INT_MAP_INT&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 26%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 26%] Built target Subgraphs make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target ShapeHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 26%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp [ 26%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 26%] Built target PartialCharges make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target MolCatalog make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 26%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 26%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 27%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/MolCatalogParams.cpp [ 27%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2018.09.1 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector RDKit::MolShapes::getConfDimensions(const RDKit::Conformer&, double, const RDGeom::Point3D*, bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2018.09.1 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 27%] Built target MolCatalog make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= Scanning dependencies of target MolInterchange make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 27%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/rapidjson -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Parser.cpp [ 28%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2018.09.1 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2018.09.1 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 28%] Built target ShapeHelpers make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target SLNParse make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNParse.cpp [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.cpp [ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 28%] Built target rdMolTransforms make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= Scanning dependencies of target rdtrajectory make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 28%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Trajectory.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Parser.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Parser.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Parser.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function.hpp:30, from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /usr/include/boost/algorithm/string/find_iterator.hpp:24, from /usr/include/boost/algorithm/string/iter_find.hpp:27, from /usr/include/boost/algorithm/string/split.hpp:16, from /usr/include/boost/algorithm/string.hpp:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::Dict::setPODVal(const string&, T) [with T = int]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNParse.cpp:35: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void RDKit::SLNParse::finalizeQueryMol(RDKit::ROMol*, bool)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Parser.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector > RDKit::MolInterchange::{anonymous}::DocToMols(rapidjson::Document&, const RDKit::MolInterchange::JSONParseParameters&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::__cxx11::string RDKit::MolToSmarts(RDKit::ROMol&, bool)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o [ 28%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.cpp cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/rapidjson -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Writer.cpp [ 29%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNAttribs.cpp [ 29%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/rdTrajectory.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function.hpp:30, from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /usr/include/boost/algorithm/string/find_iterator.hpp:24, from /usr/include/boost/algorithm/string/iter_find.hpp:27, from /usr/include/boost/algorithm/string/split.hpp:16, from /usr/include/boost/algorithm/string.hpp:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function.hpp:30, from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /usr/include/boost/algorithm/string/find_iterator.hpp:24, from /usr/include/boost/algorithm/string/iter_find.hpp:27, from /usr/include/boost/algorithm/string/split.hpp:16, from /usr/include/boost/algorithm/string.hpp:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function.hpp:30, from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /usr/include/boost/algorithm/string/find_iterator.hpp:24, from /usr/include/boost/algorithm/string/iter_find.hpp:27, from /usr/include/boost/algorithm/string/split.hpp:16, from /usr/include/boost/algorithm/string.hpp:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 29%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 29%] Built target rdtrajectory make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= Scanning dependencies of target rdqueries make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 29%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/rdqueries.cpp In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function.hpp:30, from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /usr/include/boost/algorithm/string/find_iterator.hpp:24, from /usr/include/boost/algorithm/string/iter_find.hpp:27, from /usr/include/boost/algorithm/string/split.hpp:16, from /usr/include/boost/algorithm/string.hpp:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&) [with Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNAttribs.h:39, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNAttribs.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 29%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2018.09.1 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2018.09.1 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 29%] Built target MolInterchange make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target rdChemicalFeatures make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 29%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp [ 29%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 29%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/sln.tab.cpp smarts.yy: In function 'void yysmarts_error(const char*, std::vector*, RDKit::Atom*&, RDKit::Bond*&, void*, int, const char*)': smarts.yy:24:29: warning: unused parameter 'input' [-Wunused-parameter] smarts.yy:25:46: warning: unused parameter 'ms' [-Wunused-parameter] smarts.yy:26:31: warning: unused parameter 'lastAtom' [-Wunused-parameter] smarts.yy:27:31: warning: unused parameter 'lastBond' [-Wunused-parameter] smarts.yy:28:9: warning: unused parameter 'scanner' [-Wunused-parameter] smarts.yy:28:21: warning: unused parameter 'start_token' [-Wunused-parameter] [ 30%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Queries.cpp [ 30%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp In file included from /usr/include/c++/8/vector:69, from smarts.yy:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ sln.yy: In function 'void yysln_error(const char*, std::vector*, bool, void*, const char*)': sln.yy:60:43: warning: unused parameter 'ms' [-Wunused-parameter] sln.yy:60:51: warning: unused parameter 'doQ' [-Wunused-parameter] sln.yy:61:13: warning: unused parameter 'scanner' [-Wunused-parameter] In file included from /usr/include/c++/8/vector:69, from sln.yy:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 30%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/lex.yysln.cpp smiles.yy: In function 'void yysmiles_error(const char*, std::vector*, RDKit::Atom*&, RDKit::Bond*&, std::__cxx11::list*, void*, int, const char*)': smiles.yy:38:29: warning: unused parameter 'input' [-Wunused-parameter] smiles.yy:40:31: warning: unused parameter 'lastAtom' [-Wunused-parameter] smiles.yy:41:31: warning: unused parameter 'lastBond' [-Wunused-parameter] smiles.yy:42:42: warning: unused parameter 'branchPoints' [-Wunused-parameter] smiles.yy:43:9: warning: unused parameter 'scanner' [-Wunused-parameter] smiles.yy:43:21: warning: unused parameter 'start_token' [-Wunused-parameter] smiles.yy: In function 'void yysmiles_error(const char*, std::vector*, std::__cxx11::list*, void*, int, const char*)': smiles.yy:50:29: warning: unused parameter 'input' [-Wunused-parameter] smiles.yy:52:42: warning: unused parameter 'branchPoints' [-Wunused-parameter] smiles.yy:53:9: warning: unused parameter 'scanner' [-Wunused-parameter] smiles.yy:53:21: warning: unused parameter 'start_token' [-Wunused-parameter] In file included from /usr/include/c++/8/vector:69, from smiles.yy:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 30%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 30%] Built target rdChemicalFeatures make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= Scanning dependencies of target Optimizer make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 30%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/BFGSOpt.cpp /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp: In function 'void yy_fatal_error(const char*, yyscan_t)': /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp:2585:58: warning: unused parameter 'yyscanner' [-Wunused-parameter] /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp: In function 'void* yysln_alloc(yy_size_t, yyscan_t)': /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp:2917:47: warning: unused parameter 'yyscanner' [-Wunused-parameter] /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp: In function 'void* yysln_realloc(void*, yy_size_t, yyscan_t)': /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp:2922:62: warning: unused parameter 'yyscanner' [-Wunused-parameter] /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp: In function 'void yysln_free(void*, yyscan_t)': /Users/landrgr1/RDKit_git/Code/GraphMol/SLNParse/lex.yysln.cpp:2934:40: warning: unused parameter 'yyscanner' [-Wunused-parameter] [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/lex.yysmarts.cpp [ 31%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/LinearSearch.cpp [ 31%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2018.09.1 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.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2018.09.1 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 31%] Built target SLNParse make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= Scanning dependencies of target Depictor make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 31%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.cpp [ 32%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2018.09.1 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 32%] Built target Optimizer make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target rdPartialCharges make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 33%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Built target rdqueries make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target rdShapeHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'unsigned int RDDepict::copyCoordinate(RDKit::ROMol&, std::__cxx11::list&, bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'unsigned int RDKit::CoordGen::addCoords(T&, const RDKit::CoordGen::CoordGenParams*) [with T = RDKit::ROMol]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'unsigned int RDDepict::compute2DCoords(RDKit::ROMol&, const INT_POINT2D_MAP*, bool, bool, unsigned int, unsigned int, int, bool, bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 33%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from smiles.ll:25: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'int yysmiles_lex(YYSTYPE*, yyscan_t, int&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Built target rdPartialCharges make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolInterchange make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/rapidjson -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 33%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Built target SmilesParse make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= Scanning dependencies of target testOptimizer make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/testOptimizer.cpp In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:13: /build/rdkit-201809.1+dfsg/Code/Geometry/point.h: In function 'boost::python::tuple RDKit::getUnionOfTwoBox(boost::python::tuple, boost::python::tuple)': /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:31: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:43: warning: '*((void*)(&)+16).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:55: warning: '*((void*)(&)+16).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:31: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:43: warning: '*((void*)(&)+16).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:55: warning: '*((void*)(&)+16).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:31: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:43: warning: '*((void*)(&)+16).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:55: warning: '*((void*)(&)+16).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:31: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:43: warning: '*((void*)(&)+16).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:56:55: warning: '*((void*)(&)+16).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] : Point(other), x(other.x), y(other.y), z(other.z) {} ~~~~~~^ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Snapshot.h:14, from /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/BFGSOpt.h:13, from /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/testOptimizer.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Snapshot.h:14, from /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/BFGSOpt.h:13, from /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/testOptimizer.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In function 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.cpp:10: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2146:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.cpp:10: /usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 33%] Linking CXX executable testOptimizer cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Built target testOptimizer make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ForceField /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::reflectIfNecessaryThirdPt(RDDepict::EmbeddedFrag&, unsigned int, unsigned int, unsigned int)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, Scanning dependencies of target ForceField make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::reflectIfNecessaryDensity(RDDepict::EmbeddedFrag&, unsigned int, unsigned int)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/ForceField.cpp /usr/include/c++/8/bits/stl_map.h: In member function 'RDGeom::Transform2D RDDepict::EmbeddedFrag::computeTwoAtomTrans(unsigned int, unsigned int, const INT_POINT2D_MAP&)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::updateNewNeighs(unsigned int)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/map:60, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.cpp:10: /usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.cpp:10: /usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::addAtomToAtomWithAng(unsigned int, unsigned int)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 34%] Built target rdShapeHelpers make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolqueryTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::computeNbrsAndAng(unsigned int, const INT_VECT&)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 35%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/querytest.cpp /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::permuteBonds(unsigned int, unsigned int, unsigned int)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::initFromRingCoords(const INT_VECT&, const INT_POINT2D_MAP&)': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In constructor 'RDDepict::EmbeddedFrag::EmbeddedFrag(const RDKit::ROMol*, const INT_POINT2D_MAP&)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::reflectIfNecessaryCisTrans(RDDepict::EmbeddedFrag&, unsigned int, unsigned int, unsigned int)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::flipAboutBond(unsigned int, bool)': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::mergeRing(const RDDepict::EmbeddedFrag&, unsigned int, const INT_VECT&)': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'RDGeom::Transform2D RDDepict::EmbeddedFrag::computeOneAtomTrans(unsigned int, const RDDepict::EmbeddedFrag&)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::mergeFragsWithComm(std::__cxx11::list&)': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::expandEfrag(RDKit::INT_LIST&, std::__cxx11::list&)': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 35%] Built target rdMolInterchange make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolcpTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 35%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/cptest.cpp /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::removeCollisionsShortenBonds()': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/ForceField/ForceField.h:14, from /build/rdkit-201809.1+dfsg/Code/ForceField/ForceField.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_map.h: In member function 'void RDDepict::EmbeddedFrag::randomSampleFlipsAndPermutations(unsigned int, unsigned int, int, const DOUBLE_SMART_PTR*, double, bool)': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/ForceField/ForceField.h:14, from /build/rdkit-201809.1+dfsg/Code/ForceField/ForceField.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In member function 'double ForceFields::ForceField::calcEnergy(std::vector*) const': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 36%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/DepictUtils.cpp /usr/include/c++/8/bits/stl_vector.h: In function 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleBend.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/querytest.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/cptest.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/cptest.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/DepictUtils.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/BondStretch.cpp [ 36%] Linking CXX executable graphmolcpTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 36%] Built target graphmolcpTest make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestCanon make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 36%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/testCanon.cpp In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/DepictUtils.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'RDDepict::INT_PAIR_VECT RDDepict::findBondsPairsToPermuteDeg4(const RDGeom::Point2D&, const INT_VECT&, const VECT_C_POINT&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 36%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2018.09.1 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 36%] Built target Depictor make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolMemTest1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 36%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/memtest1.cpp [ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Nonbonded.cpp [ 36%] Linking CXX executable graphmolqueryTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 36%] Built target graphmolqueryTest make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolIterTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 37%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/itertest.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/testCanon.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::RDProps::clearProp(const string&) const': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 37%] Linking CXX executable graphmoltestCanon cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestCanon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o -o graphmoltestCanon ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 37%] Built target graphmoltestCanon make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= Scanning dependencies of target test-valgrind make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 38%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/test-valgrind.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Inversion.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/memtest1.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 38%] Linking CXX executable graphmolMemTest1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 38%] Built target graphmolMemTest1 make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target ChemTransforms make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 38%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.cpp [ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/TorsionAngle.cpp [ 38%] Linking CXX executable test-valgrind cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -o test-valgrind ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser [ 38%] Linking CXX executable graphmolIterTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 38%] Built target test-valgrind make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= Scanning dependencies of target smaTest1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 38%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/smatest.cpp [ 38%] Built target graphmolIterTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= Scanning dependencies of target smiTest2 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 39%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/test2.cpp [ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/DistanceConstraint.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::{anonymous}::updateSubMolConfs(const RDKit::ROMol&, RDKit::RWMol&, boost::dynamic_bitset<>&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::ROMol* RDKit::combineMols(const RDKit::ROMol&, const RDKit::ROMol&, RDGeom::Point3D)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 40%] Linking CXX executable smiTest2 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 40%] Built target smiTest2 make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target FilterCatalog make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Filters.cpp [ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleConstraint.cpp /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::ROMol* RDKit::replaceCore(const RDKit::ROMol&, const RDKit::ROMol&, const MatchVectType&, bool, bool, bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 41%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.cpp [ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.cpp [ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/TorsionConstraint.cpp [ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/PositionConstraint.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::ROMol* RDKit::MolFragmenter::fragmentOnBonds(const RDKit::ROMol&, const std::vector&, bool, const std::vector >*, const std::vector*, std::vector*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Params.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.cpp:32: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 42%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 42%] Built target ChemTransforms make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target Fingerprints make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void boost::archive::detail::iserializer::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::text_iarchive; T = RDKit::FilterCatalogEntry]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleBend.cpp [ 43%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp [ 43%] Linking CXX executable smaTest1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 43%] Built target smaTest1 make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= Scanning dependencies of target testSubgraphs1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 43%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/test1.cpp In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h:17, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:22, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:21, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/8/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/set:60, from /build/rdkit-201809.1+dfsg/Code/Query/SetQuery.h:13, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:29, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator > > >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h:17, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:22, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:21, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/8/bits/stl_algo.h: In function 'RDKit::SparseIntVect* RDKit::getUnfoldedRDKFingerprintMol(const RDKit::ROMol&, unsigned int, unsigned int, bool, bool, bool, std::vector*, const std::vector*, std::vector >*, std::map > >*)': /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:26, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator > > >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/BondStretch.cpp [ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/PatternFingerprints.cpp [ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/StretchBend.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Filters.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp:32: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 44%] Linking CXX executable testSubgraphs1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 44%] Built target testSubgraphs1 [ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganFingerprints.cpp [ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/OopBend.cpp [ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 44%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.cpp [ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/TorsionAngle.cpp [ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MACCS.cpp In file included from /usr/include/c++/8/set:60, from /build/rdkit-201809.1+dfsg/Code/Query/SetQuery.h:13, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:29, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairs.cpp:11: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:26, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairs.cpp:11: /usr/include/c++/8/bits/stl_map.h: In function 'RDKit::SparseIntVect* RDKit::AtomPairs::getTopologicalTorsionFingerprint(const RDKit::ROMol&, unsigned int, const std::vector*, const std::vector*, const std::vector*, bool)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In function 'void RDKit::AtomPairs::{anonymous}::TorsionFpCalc(T*, const RDKit::ROMol&, unsigned int, unsigned int, const std::vector*, const std::vector*, const std::vector*, bool) [with T = RDKit::SparseIntVect]': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp [ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Nonbonded.cpp [ 44%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp: In instantiation of 'SparseBitVect* RDKit::FingerprintGenerator::getSparseFingerprint(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*) const [with OutputType = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:329:61: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:230:24: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] if (val.second >= dp_fingerprintArguments->d_countBounds[i]) { ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp: In instantiation of 'SparseBitVect* RDKit::FingerprintGenerator::getSparseFingerprint(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:337:61: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:230:24: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp: In instantiation of 'ExplicitBitVect* RDKit::FingerprintGenerator::getFingerprint(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*) const [with OutputType = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:360:61: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:293:24: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] if (val.second >= dp_fingerprintArguments->d_countBounds[i]) { ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp: In instantiation of 'ExplicitBitVect* RDKit::FingerprintGenerator::getFingerprint(const RDKit::ROMol&, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:367:61: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:293:24: warning: comparison of integer expressions of different signedness: 'int' and 'const value_type' {aka 'const unsigned int'} [-Wsign-compare] [ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/DistanceConstraint.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:33: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void RDKit::{anonymous}::hierarchy_create()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp [ 45%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 45%] Built target FilterCatalog make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= Scanning dependencies of target testSubgraphs2 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 45%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/test2.cpp [ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp [ 45%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleConstraint.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp: In instantiation of 'std::vector*> RDKit::AtomPair::AtomPairEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:133:1: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:138:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:139:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:140:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp: In instantiation of 'std::vector*> RDKit::AtomPair::AtomPairEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:133:1: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:138:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:139:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:140:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp: In instantiation of 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:83:12: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:86:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp: In instantiation of 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:83:12: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:86:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::MorganFingerprint::getMorganGenerator(unsigned int, bool, bool, bool, bool, RDKit::AtomInvariantsGenerator*, RDKit::BondInvariantsGenerator*, uint32_t, std::vector, bool, bool) [with OutputType = unsigned int; uint32_t = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:409:57: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:376:43: warning: unused parameter 'ownsBondInvGen' [-Wunused-parameter] const bool ownsAtomInvGen, const bool ownsBondInvGen) { ~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::MorganFingerprint::getMorganGenerator(unsigned int, bool, bool, bool, bool, RDKit::AtomInvariantsGenerator*, RDKit::BondInvariantsGenerator*, uint32_t, std::vector, bool, bool) [with OutputType = long long unsigned int; uint32_t = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:418:57: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:376:43: warning: unused parameter 'ownsBondInvGen' [-Wunused-parameter] [ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'std::vector*> RDKit::MorganFingerprint::MorganEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:156:1: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:159:39: warning: unused parameter 'ignoreAtoms' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:159:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:160:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:163:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'std::vector*> RDKit::MorganFingerprint::MorganEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:156:1: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:159:39: warning: unused parameter 'ignoreAtoms' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:159:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:160:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:163:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'OutputType RDKit::MorganFingerprint::MorganAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:136:12: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:137:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:138:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:139:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:140:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp: In instantiation of 'OutputType RDKit::MorganFingerprint::MorganAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:136:12: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:137:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:138:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:139:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.cpp:140:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ [ 46%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/TorsionConstraint.cpp [ 47%] Linking CXX executable testSubgraphs2 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 47%] Built target testSubgraphs2 make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target FragCatalog make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 47%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp: In instantiation of 'std::vector*> RDKit::RDKitFP::RDKitFPEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:111:1: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:114:39: warning: unused parameter 'ignoreAtoms' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:114:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:115:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:117:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:118:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp: In instantiation of 'std::vector*> RDKit::RDKitFP::RDKitFPEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:111:1: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:114:39: warning: unused parameter 'ignoreAtoms' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:114:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:115:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:117:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:118:16: warning: unused parameter 'hashResults' [-Wunused-parameter] const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp: In instantiation of 'OutputType RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:90:12: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:91:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:92:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:93:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:94:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:94:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp: In instantiation of 'OutputType RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:90:12: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:91:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:92:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:93:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:94:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:94:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ [ 47%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintUtil.cpp [ 47%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp [ 47%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/PositionConstraint.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11: /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp: In instantiation of 'RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(bool, uint32_t, bool, std::vector, uint32_t) [with OutputType = long long unsigned int; uint32_t = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:161:7: required from 'RDKit::FingerprintGenerator* RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(bool, uint32_t, RDKit::AtomInvariantsGenerator*, bool, std::vector, uint32_t, bool) [with OutputType = long long unsigned int; uint32_t = unsigned int]' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:183:58: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:26:18: warning: 'RDKit::TopologicalTorsion::TopologicalTorsionArguments::d_torsionAtomCount' will be initialized after [-Wreorder] const uint32_t d_torsionAtomCount; ^~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:27:76: warning: base 'RDKit::FingerprintArguments' [-Wreorder] FingerprintArguments(countSimulation, countBounds, fpSize){}; ^ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:21:1: warning: when initialized here [-Wreorder] TopologicalTorsionArguments::TopologicalTorsionArguments( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'RDKit::ROMol* RDKit::{anonymous}::getSmarts(const string&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp: In instantiation of 'std::vector*> RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator::getEnvironments(const RDKit::ROMol&, RDKit::FingerprintArguments*, const std::vector*, const std::vector*, int, const RDKit::AdditionalOutput*, const std::vector*, const std::vector*, bool) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:58:1: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:61:62: warning: unused parameter 'confId' [-Wunused-parameter] const std::vector *ignoreAtoms, const int confId, ~~~~~~~~~~^~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:62:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:64:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp: In instantiation of 'OutputType RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool) const [with OutputType = long long unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:43:12: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:44:39: warning: unused parameter 'arguments' [-Wunused-parameter] FingerprintArguments *arguments, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:45:39: warning: unused parameter 'atomInvariants' [-Wunused-parameter] const std::vector *atomInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:46:39: warning: unused parameter 'bondInvariants' [-Wunused-parameter] const std::vector *bondInvariants, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:47:29: warning: unused parameter 'additionalOutput' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:47:58: warning: unused parameter 'hashResults' [-Wunused-parameter] const AdditionalOutput *additionalOutput, const bool hashResults) const { ~~~~~~~~~~~^~~~~~~~~~~ [ 47%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.cpp make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target testPartialCharges make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 47%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/test1.cpp [ 48%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.cpp [ 48%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2018.09.1 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/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.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Built target Fingerprints make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target MolChemicalFeatures make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.h:19, from /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFPBCI&}; _Tp = ForceFields::MMFF::MMFFPBCI; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFChg&}; _Tp = ForceFields::MMFF::MMFFChg; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFBond&}; _Tp = ForceFields::MMFF::MMFFBond; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFHerschbachLaurie&}; _Tp = ForceFields::MMFF::MMFFHerschbachLaurie; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFCovRadPauEle&}; _Tp = ForceFields::MMFF::MMFFCovRadPauEle; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFAngle&}; _Tp = ForceFields::MMFF::MMFFAngle; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFStbn&}; _Tp = ForceFields::MMFF::MMFFStbn; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFOop&}; _Tp = ForceFields::MMFF::MMFFOop; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFTor&}; _Tp = ForceFields::MMFF::MMFFTor; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 [ 48%] Linking CXX executable testPartialCharges cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFVdW&}; _Tp = ForceFields::MMFF::MMFFVdW; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Built target testPartialCharges make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target ReducedGraphs make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.h:19, from /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFPBCICollection::MMFFPBCICollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFChgCollection::MMFFChgCollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFBondCollection::MMFFBondCollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFBndkCollection::MMFFBndkCollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/set:60, from /usr/include/boost/graph/adjacency_list.hpp:19, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFHerschbachLaurieCollection::MMFFHerschbachLaurieCollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:18, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:21, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/8/bits/stl_map.h: In function 'unsigned int RDKit::addOrder1Paths(RDKit::PATH_LIST&, const RDKit::ROMol&, RDKit::FragCatalog*, RDKit::DOUBLE_INT_MAP&, const MatchVectType&)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFCovRadPauEleCollection::MMFFCovRadPauEleCollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFAngleCollection::MMFFAngleCollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFStbnCollection::MMFFStbnCollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const RDKit::ROMol&, RDKit::FragCatalog*, RDKit::DOUBLE_INT_MAP&, const MatchVectType&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:18, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:21, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:11: /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFOopCollection::MMFFOopCollection(bool, std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFTorCollection::MMFFTorCollection(bool, std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'ForceFields::MMFF::MMFFVdWCollection::MMFFVdWCollection(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp [ 48%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp [ 48%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2018.09.1 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2018.09.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Built target ForceField [ 48%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatParams.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp [ 48%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2018.09.1 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2018.09.1 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Built target ReducedGraphs make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= Scanning dependencies of target SubstructLibrary make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatParams.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 48%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragFPGenerator.cpp make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target testSLNParse make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/test.cpp [ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp In file included from /usr/include/c++/8/set:60, from /usr/include/boost/graph/adjacency_list.hpp:19, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:11: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:18, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:21, from /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h:18, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:11: /usr/include/c++/8/bits/stl_map.h: In member function 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const FragCatalog&, const MatchVectType&, ExplicitBitVect*)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 49%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2018.09.1 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2018.09.1 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 49%] Built target SubstructLibrary make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target rdSLNParse make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 49%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 49%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2018.09.1 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.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2018.09.1 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 49%] Built target FragCatalog make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= Scanning dependencies of target rdchem make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/rdchem.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)': /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 [ 51%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2018.09.1 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.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2018.09.1 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 51%] Built target MolChemicalFeatures make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= Scanning dependencies of target FileParsers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/Mol2FileParser.cpp [ 52%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 52%] Built target rdSLNParse make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target ForceFieldHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 52%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/Mol2FileParser.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/Mol2FileParser.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/Mol2FileParser.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::Dict::setVal(const string&, T&) [with T = std::__cxx11::basic_string]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 52%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/Mol2FileParser.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::RWMol* RDKit::Mol2DataStreamToMol(std::istream*, bool, bool, RDKit::Mol2Type, bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Table.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp [ 53%] Linking CXX executable testSLNParse cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 53%] Built target testSLNParse make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= Scanning dependencies of target rdFingerprintGenerator make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 53%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 54%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'const std::vector RDKit::FingerprintWrapper::convertPyArgumentsForBulk(const boost::python::list&)': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:190:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] for (int i = 0; i < len; i++) { ~~^~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:17: /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/MorganWrapper.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::MorganWrapper::getMorganGenerator(unsigned int, bool, bool, bool, bool, bool, boost::python::api::object&, uint32_t, boost::python::api::object&, boost::python::api::object&) [with OutputType = long long unsigned int; uint32_t = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/MorganWrapper.cpp:121:63: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/MorganWrapper.cpp:24:50: warning: unused parameter 'includeRingMembership' [-Wunused-parameter] const bool onlyNonzeroInvariants, const bool includeRingMembership, ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:18: /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/RDKitFPWrapper.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::RDKitFPWrapper::getRDKitFPGenerator(unsigned int, unsigned int, bool, bool, bool, bool, boost::python::api::object&, uint32_t, boost::python::api::object&) [with OutputType = long long unsigned int; uint32_t = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/RDKitFPWrapper.cpp:92:63: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/RDKitFPWrapper.cpp:27:28: warning: unused variable 'bondInvariantsGenerator' [-Wunused-variable] BondInvariantsGenerator *bondInvariantsGenerator = nullptr; ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:19: /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/TopologicalTorsionWrapper.cpp: In instantiation of 'RDKit::FingerprintGenerator* RDKit::TopologicalTorsionWrapper::getTopologicalTorsionFPGenerator(bool, uint32_t, bool, boost::python::api::object&, uint32_t, boost::python::api::object&) [with OutputType = long long unsigned int; uint32_t = unsigned int]': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/TopologicalTorsionWrapper.cpp:75:63: required from here /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap/TopologicalTorsionWrapper.cpp:26:28: warning: unused variable 'bondInvariantsGenerator' [-Wunused-variable] BondInvariantsGenerator *bondInvariantsGenerator = nullptr; ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 54%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Atom.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileParser.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'bool RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 54%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::{anonymous}::ParseV3000AtomBlock(std::istream*, unsigned int&, unsigned int, RDKit::RWMol*, RDKit::Conformer*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 54%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 54%] Built target rdFingerprintGenerator make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolChemicalFeatures make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 54%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Atom.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 54%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp [ 54%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.cpp [ 54%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 54%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Bond.cpp /usr/include/c++/8/bits/vector.tcc: In function 'void RDKit::ClearSingleBondDirFlags(RDKit::ROMol&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp [ 54%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 54%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 54%] Built target ForceFieldHelpers make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target testReducedGraphs make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 54%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/test1.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h:17, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:22, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:17, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/8/bits/stl_algobase.h: In function 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator*, std::vector > >; _ForwardIterator2 = __gnu_cxx::__normal_iterator*, std::vector > >]': /usr/include/c++/8/bits/stl_algobase.h:120:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 iter_swap(_ForwardIterator1 __a, _ForwardIterator2 __b) ^~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:120:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:120:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h:17, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:22, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h:17, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:22, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:84:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::iter_swap(__result, __b); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:86:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::iter_swap(__result, __c); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:88:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::iter_swap(__result, __a); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/8/bits/vector.tcc: In function 'void RDKit::GetMolFileAtomProperties(const RDKit::Atom*, const RDKit::Conformer*, int&, int&, unsigned int&, double&, double&, double&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h:17, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:22, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileWriter.cpp:13: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Bond.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 54%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp [ 55%] Linking CXX executable testReducedGraphs cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 55%] Built target testReducedGraphs [ 55%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Mol.cpp [ 55%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Conformer.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void RDKit::ForwardSDMolSupplier::readMolProps(RDKit::ROMol*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SDMolSupplier.cpp [ 56%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -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.1.2018.09.1 ../../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 56%] Built target rdMolChemicalFeatures make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= Scanning dependencies of target rdReducedGraphs make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 56%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SDMolSupplier.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::fpos<__mbstate_t>&}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SDMolSupplier.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::SDMolSupplier::moveTo(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual RDKit::ROMol* RDKit::SDMolSupplier::next()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'unsigned int RDKit::SDMolSupplier::length()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SDWriter.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Conformer.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Conformer.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Conformer.cpp:20: /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Conformer.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::SetAtomPos(RDKit::Conformer*, unsigned int, boost::python::api::object)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 56%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 56%] Built target rdReducedGraphs [ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SmilesWriter.cpp [ 57%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/RingInfo.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/Mol.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'RDKit::ROMol* RDKit::SmilesMolSupplier::processLine(std::__cxx11::string)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TDTMolSupplier.cpp [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TDTWriter.cpp [ 58%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/EditableMol.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void RDKit::TDTParseUtils::ParseNumberList(std::__cxx11::string, std::vector&, std::istream*) [with T = double]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In member function 'RDKit::ROMol* RDKit::TDTMolSupplier::parseMol(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, from /usr/include/boost/tokenizer.hpp:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:12: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TplFileParser.cpp [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TplFileWriter.cpp make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DistGeom /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeometry make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 58%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DistGeom/DistGeomUtils.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TplFileParser.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TplFileParser.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TplFileParser.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 58%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/MonomerInfo.cpp In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/TplFileParser.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::ParseTPLAtomLine(std::__cxx11::string, unsigned int, RDKit::RWMol*, RDKit::Conformer*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::Conformer* RDKit::ParseConfData(std::istream*, unsigned int&, RDKit::RWMol*, unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/PDBWriter.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 58%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DistGeom/TriangleSmooth.cpp In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/math/special_functions/math_fwd.hpp:26, from /usr/include/boost/math/special_functions/sign.hpp:17, from /usr/include/boost/lexical_cast/detail/inf_nan.hpp:34, from /usr/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:63, from /usr/include/boost/lexical_cast/detail/converter_lexical.hpp:54, from /usr/include/boost/lexical_cast/try_lexical_convert.hpp:42, from /usr/include/boost/lexical_cast.hpp:32, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/PDBParser.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::PDBConformerLine(RDKit::RWMol*, const char*, unsigned int, RDKit::Conformer*&, int&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::PDBAtomLine(RDKit::RWMol*, const char*, unsigned int, unsigned int, std::map&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/PDBSupplier.cpp [ 58%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DistGeom/DistViolationContrib.cpp [ 58%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MaeMolSupplier.cpp [ 59%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DistGeom/ChiralViolationContrib.cpp [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 59%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2018.09.1 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../lib/libRDKitForceField.so.1.2018.09.1 ../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 59%] Built target DistGeometry make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target MolAlign make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 59%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/AlignMolecules.cpp [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceParsers.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual RDKit::ROMol* RDKit::MaeMolSupplier::next()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:13: /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceWriters.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/Numerics/Vector.h:15, from /build/rdkit-201809.1+dfsg/Code/Numerics/Matrix.h:15, from /build/rdkit-201809.1+dfsg/Code/Numerics/SquareMatrix.h:14, from /build/rdkit-201809.1+dfsg/Code/Geometry/Transform3D.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/AlignMolecules.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/AlignMolecules.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceParsers.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 59%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp /usr/include/c++/8/bits/vector.tcc: In function 'RDKit::RWMol* RDKit::FASTAToMol(const char*, bool, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 59%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/MolBundle.cpp [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SVGParser.cpp make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ForceField/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= Scanning dependencies of target rdForceField make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/Wrap/ForceField.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SVGParser.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SVGParser.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SVGParser.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SVGParser.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In function 'RDKit::RWMol* RDKit::RDKitSVGToMol(std::istream*, bool, bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 60%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2018.09.1 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o CMakeFiles/MolAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Built target MolAlign make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DistGeom /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target testDistGeom make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DistGeom/testDistGeom.cpp [ 60%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2018.09.1 CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lmaeparser ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser [ 60%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Built target FileParsers make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DistGeom/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeom make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/c++ -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/rdkit-201809.1+dfsg/Code/DistGeom/Wrap/DistGeom.cpp make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Built target rdchem make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolMolOpsTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/molopstest.cpp /build/rdkit-201809.1+dfsg/Code/ForceField/Wrap/ForceField.cpp: In member function 'double ForceFields::PyForceField::calcEnergyWithPos(const boost::python::api::object&)': /build/rdkit-201809.1+dfsg/Code/ForceField/Wrap/ForceField.cpp:135:12: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] c[i] = python::extract(pos[i]); /build/rdkit-201809.1+dfsg/Code/ForceField/Wrap/ForceField.cpp: In member function 'PyObject* ForceFields::PyForceField::calcGradWithPos(const boost::python::api::object&)': /build/rdkit-201809.1+dfsg/Code/ForceField/Wrap/ForceField.cpp:169:12: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] c[i] = python::extract(pos[i]); [ 60%] Linking CXX executable testDistGeom cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../lib/libRDKitForceField.so.1.2018.09.1 ../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Built target testDistGeom make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolTestsCatch make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/catch_tests.cpp [ 60%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 60%] Built target DistGeom make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolTest1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/test1.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 61%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 61%] Built target rdForceField make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestPicklerGlobalSetting make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/testPicklerGlobalSettings.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/test1.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/test1.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/test1.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/test1.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::RDProps::clearProp(const string&) const': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/testPicklerGlobalSettings.cpp:33: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::RDProps::clearComputedProps() const': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ [ 61%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 61%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestChirality make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 61%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/testChirality.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/catch_tests.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 61%] Linking CXX executable graphmolTest1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../lib/libRDKitForceField.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 61%] Built target graphmolTest1 make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestPickler make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/testPickler.cpp In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'void testAddHsCoords()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::Dict::setPODVal(const string&, T) [with T = int]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/testPickler.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/testPickler.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/testPickler.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void ____C_A_T_C_H____T_E_S_T____7()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/molopstest.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'void testIssue212()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 62%] Linking CXX executable graphmoltestPickler cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser /usr/include/c++/8/bits/stl_vector.h: In function 'void testAddConformers()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Built target graphmoltestPickler make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= Scanning dependencies of target molBundleTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/testMolBundle.cpp [ 62%] Linking CXX executable graphmolTestsCatch cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolTestsCatch.dir/catch_tests.cpp.o -o graphmolTestsCatch ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Built target graphmolTestsCatch make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= Scanning dependencies of target hanoiTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/hanoitest.cpp [ 62%] Linking CXX executable graphmoltestChirality cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Built target graphmoltestChirality make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= Scanning dependencies of target resMolSupplierTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/resMolSupplierTest.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/new_canon.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/hanoitest.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 62%] Linking CXX executable molBundleTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Built target molBundleTest make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= Scanning dependencies of target testDepictor make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/testDepictor.cpp /usr/include/c++/8/bits/vector.tcc: In function 'void test7()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 63%] Linking CXX executable resMolSupplierTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread [ 63%] Linking CXX executable hanoiTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target resMolSupplierTest make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= Scanning dependencies of target rdDepictor make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp [ 63%] Built target hanoiTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= Scanning dependencies of target smiTest1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/test.cpp In file included from /usr/include/c++/8/set:60, from /build/rdkit-201809.1+dfsg/Code/Query/SetQuery.h:13, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:29, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2486:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:26, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = int; _Tp = RDGeom::Point2D; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/set:60, from /build/rdkit-201809.1+dfsg/Code/Query/SetQuery.h:13, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:29, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/8/bits/stl_tree.h: In function 'void test4()': /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _M_erase_aux(__position); ^~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:26, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/testDepictor.cpp:13: /usr/include/c++/8/bits/stl_map.h: In function 'void testIssue2091304()': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In function 'void testIssue3122141()': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In function 'void testIssue2303566()': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 63%] Linking CXX executable testDepictor cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target testDepictor make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= Scanning dependencies of target cxsmilesTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/cxsmiles_test.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/test.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:17: /build/rdkit-201809.1+dfsg/Code/Geometry/point.h: In function 'unsigned int RDDepict::Compute2DCoords(RDKit::ROMol&, bool, bool, boost::python::dict&, unsigned int, unsigned int, int, bool, double, bool)': /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:289:15: warning: '*((void*)(&)+16).RDGeom::Point2D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ [ 63%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target rdDepictor make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= Scanning dependencies of target smiTestCatch make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/catch_tests.cpp [ 63%] Linking CXX executable graphmolMolOpsTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../lib/libRDKitDepictor.so.1.2018.09.1 ../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target graphmolMolOpsTest make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= Scanning dependencies of target testMol2ToMol make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 63%] Linking CXX executable cxsmilesTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target cxsmilesTest make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= Scanning dependencies of target testTplParser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testTpls.cpp [ 63%] Linking CXX executable testMol2ToMol cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= Scanning dependencies of target testMolWriter make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMolWriter.cpp [ 63%] Linking CXX executable testTplParser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= Scanning dependencies of target testMolSupplier make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMolSupplier.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMolWriter.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMolWriter.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMolWriter.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMolSupplier.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::fpos<__mbstate_t>&}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In function 'void testBug3525799()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/catch_tests.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/catch_tests.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void testGitHub23()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMolSupplier.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In function 'void testSetStreamIndices()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testMolWriter.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'void testIssue265()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 63%] Linking CXX executable testMolWriter cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= Scanning dependencies of target testSequence make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testSequence.cpp [ 63%] Linking CXX executable smiTest1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= Scanning dependencies of target testExtendedStereoParsing make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp [ 64%] Linking CXX executable testMolSupplier cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 64%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= Scanning dependencies of target fileParsersTest1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/test1.cpp [ 64%] Linking CXX executable testSequence cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 64%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= Scanning dependencies of target fileParsersCatchTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/catch_tests.cpp [ 65%] Linking CXX executable testExtendedStereoParsing cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 65%] Built target testExtendedStereoParsing make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= Scanning dependencies of target testSubstructMatch make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct/test1.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/test1.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/test1.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/test1.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 65%] Linking CXX executable smiTestCatch cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct/test1.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 65%] Built target smiTestCatch make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= Scanning dependencies of target Descriptors make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Crippen.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/catch_tests.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/catch_tests.cpp:13: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void test5QueryRoot()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Crippen.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDKit::Descriptors::CrippenParams&}; _Tp = RDKit::Descriptors::CrippenParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Crippen.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Descriptors::CrippenParamCollection::CrippenParamCollection(const string&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 65%] Linking CXX executable testSubstructMatch cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 65%] Built target testSubstructMatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testChemTransforms make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 66%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/testChemTransforms.cpp [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolDescriptors.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolSurf.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolSurf.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::Dict::setVal(const string&, const char*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Lipinski.cpp /usr/include/c++/8/bits/vector.tcc: In function 'void testMolFileAtomValues()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 66%] Linking CXX executable testChemTransforms cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 66%] Built target testChemTransforms make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= Scanning dependencies of target filterCatalogTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 66%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 66%] Linking CXX executable fileParsersCatchTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/fileParsersCatchTest.dir/catch_tests.cpp.o -o fileParsersCatchTest ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 66%] Built target fileParsersCatchTest make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdfiltercatalog make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 68%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp:33: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::Dict::setVal(const string&, const char*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/graph/adjacency_list.hpp:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:27, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 68%] Linking CXX executable filterCatalogTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 68%] Built target filterCatalogTest make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target testFragCatalog make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 68%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/test1.cpp [ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MQN.cpp [ 68%] Linking CXX executable fileParsersTest1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lmaeparser ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 68%] Built target fileParsersTest1 make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdfragcatalog make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp [ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Property.cpp [ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Property.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Property.cpp:32: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 68%] Linking CXX executable testFragCatalog cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 68%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector RDKit::Descriptors::Properties::computeProperties(const RDKit::ROMol&, bool) const': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ Scanning dependencies of target testFingerprints make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 69%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/test1.cpp [ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::FilterCatalogEntry::setProp(const string&, T) [with T = std::__cxx11::basic_string]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 69%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/test1.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 [ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/USRDescriptor.cpp [ 71%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void RDKit::RDProps::clearProp(const string&) const': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread [ 71%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2018.09.1 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target rdfiltercatalog [ 71%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target Descriptors make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= Scanning dependencies of target testFingerprintGenerators make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testMolTransforms make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:21, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:12: /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp: In function 'void testAtomPairNonSparseBitvector()': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:225:42: warning: comparison of integer expressions of different signedness: 'int' and '__gnu_cxx::__alloc_traits, unsigned int>::value_type' {aka 'unsigned int'} [-Wsign-compare] TEST_ASSERT(isSet == (it->second >= defaultCountBounds[i])); /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:152:9: note: in definition of macro 'TEST_ASSERT' if (!(expr)) { \ ^~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:242:42: warning: comparison of integer expressions of different signedness: 'int' and '__gnu_cxx::__alloc_traits, unsigned int>::value_type' {aka 'unsigned int'} [-Wsign-compare] TEST_ASSERT(isSet == (it->second >= defaultCountBounds[i])); /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h:152:9: note: in definition of macro 'TEST_ASSERT' if (!(expr)) { \ ^~~~ make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/test1.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp: In function 'void testBulkFP()': /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:2388:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector*>::size_type' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < results->size(); i++) { ~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, from /usr/include/boost/range/size_type.hpp:20, from /usr/include/boost/range/size.hpp:21, from /usr/include/boost/range/functions.hpp:20, from /usr/include/boost/range/iterator_range_core.hpp:38, from /usr/include/boost/range/iterator_range.hpp:13, from /usr/include/boost/iostreams/traits.hpp:38, from /usr/include/boost/iostreams/detail/call_traits.hpp:15, from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, from /usr/include/boost/iostreams/tee.hpp:18, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h:17, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:11: /usr/include/c++/8/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/test1.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/test1.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -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.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target rdfragcatalog make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target rdForceFieldHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp /usr/include/c++/8/bits/stl_vector.h: In function 'void test1Canonicalization()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 71%] Linking CXX executable testMolTransforms cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target testMolTransforms make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolAlign make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp [ 71%] Linking CXX executable testFingerprints cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target testFingerprints make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target testFeatures make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'RDKit::MolAlign::PyO3A* RDKit::MolAlign::getCrippenO3A(RDKit::ROMol&, RDKit::ROMol&, boost::python::list, boost::python::list, int, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:451:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] (python::len(prbCrippenContribs) == prbNAtoms)) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:466:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] (python::len(refCrippenContribs) == refNAtoms)) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'boost::python::tuple RDKit::MolAlign::getCrippenO3AForConfs(RDKit::ROMol&, RDKit::ROMol&, int, boost::python::list, boost::python::list, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:532:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] (python::len(prbCrippenContribs) == prbNAtoms)) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:547:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] (python::len(refCrippenContribs) == refNAtoms)) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:16: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:16: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void testAtomPairOutput()': /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/set:60, from /build/rdkit-201809.1+dfsg/Code/Query/SetQuery.h:13, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:29, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:12: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:26, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:12: /usr/include/c++/8/bits/stl_map.h: In function 'void testRDKitFP()': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In function 'void testTopologicalTorsionFPOld()': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target rdForceFieldHelpers make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testShapeHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:24: /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h: In function 'RDNumeric::DoubleVector* RDKit::_translateWeights(boost::python::api::object)': /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] T res = python::extract(d_seq[which]); ^~~ [ 71%] Linking CXX executable testFeatures cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target testFeatures make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target testMolCatalog make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/test1.cpp [ 71%] Linking CXX executable testFingerprintGenerators cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target testFingerprintGenerators make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolCatalog make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 72%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp [ 72%] Linking CXX executable testShapeHelpers cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2018.09.1 ../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 72%] Built target testShapeHelpers make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= Scanning dependencies of target FMCS make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/FMCS.cpp [ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 72%] Built target rdMolAlign make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= Scanning dependencies of target MolHash make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 73%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/MolHash.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolHash.dir/MolHash.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash/MolHash.cpp [ 73%] Linking CXX executable testMolCatalog cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target testMolCatalog make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= Scanning dependencies of target MMPA make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 73%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/MMPA.cpp [ 73%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/HashToString.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolHash.dir/HashToString.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash/HashToString.cpp [ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target rdMolCatalog [ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Seed.cpp [ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/MMPA.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 73%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2018.09.1 CMakeFiles/MolHash.dir/MolHash.cpp.o CMakeFiles/MolHash.dir/HashToString.cpp.o ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2018.09.1 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target MolHash [ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/SubstructMatchCustom.cpp [ 73%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2018.09.1 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2018.09.1 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target MMPA make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target StructChecker make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 73%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructChecker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/StructChecker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructChecker.cpp [ 73%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp [ 73%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StructureFlags.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/StructureFlags.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructureFlags.cpp [ 74%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Utilites.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/Utilites.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Utilites.cpp [ 74%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Pattern.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/Pattern.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Pattern.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp: In function 'bool RDKit::StructureCheck::ReadAAPairs(const string&, std::vector >&)': /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.cpp:354:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d", &n); ~~~~~~^~~~~~~~~~~~~~ [ 74%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Stereo.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/Stereo.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Stereo.cpp [ 74%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2018.09.1 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.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2018.09.1 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 74%] Built target FMCS make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 74%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/trajectoryTest.cpp [ 74%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/AtomSymbolMatch.cpp [ 74%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StripSmallFragments.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/trajectoryTest.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/ReCharge.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/ReCharge.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/ReCharge.cpp [ 75%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Tautomer.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/StructChecker.dir/Tautomer.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Tautomer.cpp /usr/include/c++/8/bits/vector.tcc: In function 'void testAddConformersFromTrajectory()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 76%] Linking CXX executable trajectoryTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target trajectoryTest make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= Scanning dependencies of target substructLibraryTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/../MolOps.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StripSmallFragments.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= Scanning dependencies of target rdSubstructLibrary make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [ 76%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 76%] Linking CXX shared library ../../../lib/libRDKitStructChecker.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/cmake -E cmake_link_script CMakeFiles/StructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitStructChecker.so.1 -o ../../../lib/libRDKitStructChecker.so.1.2018.09.1 CMakeFiles/StructChecker.dir/StructChecker.cpp.o CMakeFiles/StructChecker.dir/StructCheckerOptions.cpp.o CMakeFiles/StructChecker.dir/StructureFlags.cpp.o CMakeFiles/StructChecker.dir/Utilites.cpp.o CMakeFiles/StructChecker.dir/Pattern.cpp.o CMakeFiles/StructChecker.dir/Stereo.cpp.o CMakeFiles/StructChecker.dir/AtomSymbolMatch.cpp.o CMakeFiles/StructChecker.dir/StripSmallFragments.cpp.o CMakeFiles/StructChecker.dir/ReCharge.cpp.o CMakeFiles/StructChecker.dir/Tautomer.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitStructChecker.so.1.2018.09.1 ../../../lib/libRDKitStructChecker.so.1 ../../../lib/libRDKitStructChecker.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target StructChecker make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= Scanning dependencies of target RGroupDecomposition make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= Scanning dependencies of target molInterchangeTest1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/rapidjson -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/test1.cpp [ 76%] Linking CXX executable substructLibraryTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target substructLibraryTest make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= Scanning dependencies of target rdmolfiles make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/rdmolfiles.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp:31: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/test1.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 76%] Linking CXX executable molInterchangeTest1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lpthread -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target molInterchangeTest1 [ 76%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp [ 76%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2018.09.1 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o ../../../lib/libRDKitFMCS.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2018.09.1 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target RGroupDecomposition make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ForceField/UFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= Scanning dependencies of target testUFFForceField make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/testUFFForceField.cpp [ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2018.09.1 ../../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target rdSubstructLibrary [ 76%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/MaeMolSupplier.cpp In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:23: /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:185:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:155:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target DistGeomHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp [ 76%] Linking CXX executable testUFFForceField cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target testUFFForceField make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= Scanning dependencies of target ChemReactions make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 77%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.cpp make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= Scanning dependencies of target testDescriptors make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/test.cpp In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/MaeMolSupplier.cpp:21: /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekpos(boost_adaptbx::python::streambuf::pos_type, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:185:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:155:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ [ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/SDMolSupplier.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:37, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.cpp:33: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/MDLParser.cpp [ 78%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.cpp In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/SDMolSupplier.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void RDKit::setStreamIndices(RDKit::SDMolSupplier&, boost::python::api::object)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/TDTMolSupplier.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::DGeomHelpers::detail::embedHelper_(int, int, RDKit::DGeomHelpers::detail::EmbedArgs*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 79%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 79%] Built target DistGeomHelpers make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= Scanning dependencies of target testAUTOCORR2D make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp [ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionPickler.cpp [ 79%] Linking CXX executable testDescriptors cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 79%] Built target testDescriptors make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolDescriptors make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 79%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDescriptors_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp [ 79%] Linking CXX executable testAUTOCORR2D cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 79%] Built target testAUTOCORR2D make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testMMFFForceFieldHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 79%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/SmilesMolSupplier.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp:15: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp:15: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionWriter.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:37, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionWriter.cpp:33: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void {anonymous}::setRXNRoleOfAllMoleculeAtoms(RDKit::ROMol&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/SmilesWriter.cpp [ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionDepict.cpp [ 79%] Linking CXX executable testMMFFForceFieldHelpers cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 79%] Built target testMMFFForceFieldHelpers [ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/SDWriter.cpp In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:12: /build/rdkit-201809.1+dfsg/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributionsFromPoints(boost::python::api::object, boost::python::api::object)': /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:85:15: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:86:15: warning: '*((void*)(&)+16).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] y = other.y; ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+16).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] z = other.z; ~~~~~~^ [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp /build/rdkit-201809.1+dfsg/Code/Geometry/point.h: In function 'boost::python::list {anonymous}::GetUSRDistributions(boost::python::api::object, boost::python::api::object)': /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:85:15: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:86:15: warning: '*((void*)(&)+16).RDGeom::Point3D::y' may be used uninitialized in this function [-Wmaybe-uninitialized] y = other.y; ~~~~~~^ /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:87:15: warning: '*((void*)(&)+16).RDGeom::Point3D::z' may be used uninitialized in this function [-Wmaybe-uninitialized] z = other.z; ~~~~~~^ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/SmilesWriter.cpp:20: /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:185:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:155:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/SDWriter.cpp:21: /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:185:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:155:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionUtils.cpp [ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/TDTWriter.cpp [ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/PDBWriter.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:37, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionUtils.cpp:34: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/MoleculeParser.cpp In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/TDTWriter.cpp:21: /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:185:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:155:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/PDBWriter.cpp:20: /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:185:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:155:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ [ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.cpp make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testUFFForceFieldHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp [ 81%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Built target rdmolfiles make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= Scanning dependencies of target testCrystalForceField make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp [ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Built target rdMolDescriptors make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target testDistGeomHelpers make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:37, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.cpp:33: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:37, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.cpp:33: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::ReactionRunnerUtils::generateProductConformers(RDKit::Conformer*, const RDKit::ROMol&, RDKit::ReactionRunnerUtils::ReactantProductAtomMapping*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:37, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.cpp:33: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 81%] Linking CXX executable testCrystalForceField cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp:15: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp:15: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ [ 81%] Built target testCrystalForceField make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= Scanning dependencies of target rdDistGeom make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 82%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp [ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/PreprocessRxn.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:13: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 82%] Linking CXX executable testUFFForceFieldHelpers cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread [ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.cpp make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 82%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= Scanning dependencies of target testMolAlign make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 82%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/testMolAlign.cpp In file included from /usr/include/c++/8/map:60, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:17: /build/rdkit-201809.1+dfsg/Code/Geometry/point.h: In function 'RDKit::INT_VECT RDKit::EmbedMultipleConfs(RDKit::ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool)': /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:85:15: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ In file included from /usr/include/c++/8/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:17: /build/rdkit-201809.1+dfsg/Code/Geometry/point.h: In function 'int RDKit::EmbedMolecule(RDKit::ROMol&, unsigned int, int, bool, bool, double, bool, unsigned int, boost::python::dict&, double, bool, bool, bool, bool, bool)': /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:85:15: warning: '*((void*)(&)+16).RDGeom::Point3D::x' may be used uninitialized in this function [-Wmaybe-uninitialized] x = other.x; ~~~~~~^ In file included from /usr/include/c++/8/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h:3, from /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/vector.tcc: In function 'void testGithub568()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:37, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h:36, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.cpp:32: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 ../../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 82%] Built target rdDistGeom make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= Scanning dependencies of target testFMCS make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 82%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/testFMCS_Unit.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/Numerics/Vector.h:15, from /build/rdkit-201809.1+dfsg/Code/Numerics/Matrix.h:15, from /build/rdkit-201809.1+dfsg/Code/Numerics/SquareMatrix.h:14, from /build/rdkit-201809.1+dfsg/Code/Geometry/Transform3D.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/AlignMolecules.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/testMolAlign.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 82%] Linking CXX executable testDistGeomHelpers cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 ../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 82%] Built target testDistGeomHelpers make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= Scanning dependencies of target rdFMCS make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 82%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp [ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/testFMCS_Unit.cpp:48: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 84%] Linking CXX executable testMolAlign cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 ../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 84%] Built target testMolAlign make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= Scanning dependencies of target FMCStest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::__cxx11::string testChEMBL_Txt(const char*, double, const char*)': /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:501:17: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(fres, "%s;%lu;%.1f;%.4f;%u;%u;%s;", test, mols.size(), th, sec, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1172:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1184:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1279:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1328:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:1408:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ [ 85%] Linking CXX executable testFMCS cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Built target testFMCS make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/DependInfo.cmake --color= Scanning dependencies of target testMolHash make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/testMolHash.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMolHash.dir/testMolHash.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash/testMolHash.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/../../RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test/testFMCS.cpp:48: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void test504()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 85%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Built target rdFMCS make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolHash make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 85%] Linking CXX executable FMCStest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Built target FMCStest make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= Scanning dependencies of target testMMPA make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/MMPA_UnitTest.cpp [ 85%] Linking CXX executable testMolHash cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMolHash.dir/testMolHash.cpp.o -o testMolHash ../../../lib/libRDKitMolHash.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Built target testMolHash make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= Scanning dependencies of target rdMMPA make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 86%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp [ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2018.09.1 ../../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 87%] Built target rdMolHash make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target testStructChecker make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 87%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_STRUCTCHECKER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 87%] Built target testMMPA make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/DependInfo.cmake --color= Scanning dependencies of target rdStructChecker make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 87%] Building CXX object Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/structchecker.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdStructChecker_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdStructChecker.dir/structchecker.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Wrap/structchecker.cpp [ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 87%] Built target rdMMPA make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= Scanning dependencies of target testRGroupDecomp make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make 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CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp [ 87%] Linking CXX executable testStructChecker cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker && /usr/bin/cmake -E cmake_link_script CMakeFiles/testStructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testStructChecker.dir/testStructChecker.cpp.o -o testStructChecker ../../../lib/libRDKitStructChecker.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 87%] Built target testStructChecker make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= Scanning dependencies of target rdRGroupDecomposition make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 87%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 87%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2018.09.1 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 87%] Built target ChemReactions make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= Scanning dependencies of target testMMFFForceField make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/testMMFFForceField.cpp [ 88%] Linking CXX shared module ../../../../rdkit/Chem/rdStructChecker.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdStructChecker.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdStructChecker.so CMakeFiles/rdStructChecker.dir/structchecker.cpp.o ../../../../lib/libRDKitStructChecker.so.1.2018.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 88%] Built target rdStructChecker make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= Scanning dependencies of target testReaction make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 88%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/testReaction.cpp [ 88%] Linking CXX executable testRGroupDecomp cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2018.09.1 ../../../lib/libRDKitFMCS.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 88%] Built target testRGroupDecomp make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= Scanning dependencies of target testEnumeration make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp [ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2018.09.1 ../../../../lib/libRDKitFMCS.so.1.2018.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Built target rdRGroupDecomposition make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target testReactionFingerprints make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp [ 89%] Linking CXX executable testEnumeration cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Built target testEnumeration make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/testReaction.cpp:34: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ Scanning dependencies of target rxnTestCatch make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/catch_tests.cpp In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/testReaction.cpp:34: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/testReaction.cpp:34: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 89%] Linking CXX executable testMMFFForceField cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2018.09.1 ../../../lib/libRDKitDistGeometry.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitMolAlign.so.1.2018.09.1 ../../../lib/libRDKitAlignment.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2018.09.1 ../../../lib/libRDKitForceField.so.1.2018.09.1 ../../../lib/libRDKitOptimizer.so.1.2018.09.1 ../../../lib/libRDKitTrajectory.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Built target testMMFFForceField make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= Scanning dependencies of target rdChemReactions make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp [ 89%] Linking CXX executable testReactionFingerprints cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Built target testReactionFingerprints make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= Scanning dependencies of target MolDraw2D make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In constructor 'RDKit::Conformer::Conformer(unsigned int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:19, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In member function 'void RDKit::MolDraw2D::extractAtomCoords(const RDKit::ROMol&, int, bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/catch_tests.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/External/catch/catch/single_include/catch.hpp:465, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/catch_tests.cpp:12: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void RDKit::MolDraw2D::drawReaction(const RDKit::ChemicalReaction&, bool, const std::vector >*, const std::vector*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/stl_vector.h: In function 'void boost::python::container_utils::extend_container(Container&, boost::python::api::object) [with Container = std::vector]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]': /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/boost/function/detail/prologue.hpp:13, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In static member function 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]': /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void boost::python::vector_indexing_suite::base_extend(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]': /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]': /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/vector.tcc:149:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(begin() + (__position - cbegin()), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/vector.tcc:149:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(begin() + (__position - cbegin()), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/detail/container_fwd.hpp:93, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/function/function_base.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:31: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap.h:24, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:689:9: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:689:9: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:689:9: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:689:9: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 [ 89%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp:11: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp:11: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::MolDraw2D_detail::arcPoints(const RDGeom::Point2D&, const RDGeom::Point2D&, std::vector&, float, float)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp [ 89%] Linking CXX executable rxnTestCatch cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 89%] Built target rxnTestCatch make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= Scanning dependencies of target MolStandardize make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/MolStandardize.cpp [ 90%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2018.09.1 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread -lboost_serialization cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2018.09.1 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 90%] Built target MolDraw2D [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Metal.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:32: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/rdkit-201809.1+dfsg/Code/Geometry/point.h:16, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:32: /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::MolClearComputedProps(const RDOb&) [with RDOb = RDKit::ChemicalReaction]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h: In function 'void RDKit::MolClearProp(const RDOb&, const char*) [with RDOb = RDKit::ChemicalReaction]': /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Normalize.cpp [ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Validate.cpp [ 91%] Linking CXX executable testReaction cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lcoordgenlibs -lmaeparser [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Charge.cpp make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 91%] Built target testReaction make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= Scanning dependencies of target moldraw2DTest1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/test1.cpp [ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Tautomer.cpp [ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Fragment.cpp [ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:21, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp [ 93%] Built target rdChemReactions make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= Scanning dependencies of target moldraw2DRxnTest1 make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/rxn_test1.cpp /usr/include/c++/8/bits/vector.tcc: In function 'void testGithub1322()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolDraw2D make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 93%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp In file included from /usr/include/c++/8/map:60, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h:19, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h:28, from /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h:15, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/test1.cpp:12: /usr/include/c++/8/bits/stl_map.h: In function 'void test3()': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, [ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp [ 94%] Linking CXX executable moldraw2DTest1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 94%] Built target moldraw2DTest1 [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp [ 94%] Linking CXX executable moldraw2DRxnTest1 cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 94%] Built target moldraw2DRxnTest1 make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= Scanning dependencies of target rdmolops make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/rdmolops.cpp [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector > RDKit::MolStandardize::readFuncGroups(std::istream&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp [ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/MolOps.cpp [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:54:57: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] double r = python::extract(tDict.values()[i]); ^ [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector, boost::shared_ptr > > RDKit::MolStandardize::readPairs(std::istream&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp [ 95%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2018.09.1 ../../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lboost_serialization make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 95%] Built target rdMolDraw2D [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ [ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp /usr/include/c++/8/bits/vector.tcc: In function 'std::vector > RDKit::MolStandardize::readTransformations(std::istream&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp In file included from /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap/MolOps.cpp:30: /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(boost_adaptbx::python::streambuf::off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:336:16: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] result = off_type(bp::extract(py_tell())); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:185:56: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h:155:58: warning: '*((void*)& +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] off_type py_pos = bp::extract(py_tell()); ^ In file included from /usr/include/c++/8/vector:69, from /build/rdkit-201809.1+dfsg/Code/Query/Query.h:18, from /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h:20, from /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h:25, from /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h:23, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h:14, from /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'RDKit::MolStandardize::TautomerTransform* RDKit::{anonymous}::getTautomer(const string&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 96%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 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.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread -lboost_serialization cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 96%] Built target MolStandardize make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= Scanning dependencies of target molStandardizeTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build Scanning dependencies of target molValidateTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Scanning dependencies of target molNormalizeTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/test1.cpp [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/testNormalize.cpp [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/testValidate.cpp [ 97%] Linking CXX executable molNormalizeTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= Scanning dependencies of target molChargeTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/testCharge.cpp [ 97%] Linking CXX executable molValidateTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= Scanning dependencies of target molStandardizeSmallTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/test2.cpp [ 97%] Linking CXX executable molStandardizeTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Built target molStandardizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= Scanning dependencies of target molTautomerTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/testTautomer.cpp [ 97%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o ../../../lib/libRDKitMolDraw2D.so.1.2018.09.1 ../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lboost_serialization make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Built target rdmolops make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= Scanning dependencies of target molFragmentTest make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/testFragment.cpp [ 98%] Linking CXX executable molChargeTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 98%] Built target molChargeTest make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolStandardize make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[4]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp [ 98%] Linking CXX executable molStandardizeSmallTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/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/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 98%] Built target molStandardizeSmallTest [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Wrap/Validate.cpp [ 98%] Linking CXX executable molFragmentTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lboost_serialization make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 98%] Built target molFragmentTest [ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Wrap/Charge.cpp [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp [ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/rdkit-201809.1+dfsg/External/catch/catch/single_include -I/build/rdkit-201809.1+dfsg/External -I/usr/include/python2.7 -I/build/rdkit-201809.1+dfsg/Code -I/build/rdkit-201809.1+dfsg/External/boost-numeric-bindings -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Wrap/Metal.cpp [ 99%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -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 ../../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../../lib/libRDKitRDBoost.so.1.2018.09.1 -lpython2.7 -lboost_python27 -lboost_serialization ../../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../../lib/libRDKitSubgraphs.so.1.2018.09.1 ../../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../../lib/libRDKitDataStructs.so.1.2018.09.1 -lcoordgenlibs -lmaeparser ../../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lpthread -lboost_serialization make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 99%] Built target rdMolStandardize [100%] Linking CXX executable molTautomerTest cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -rdynamic CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2018.09.1 ../../../lib/libRDKitChemReactions.so.1.2018.09.1 ../../../lib/libRDKitFilterCatalog.so.1.2018.09.1 ../../../lib/libRDKitCatalogs.so.1.2018.09.1 ../../../lib/libRDKitDescriptors.so.1.2018.09.1 ../../../lib/libRDKitFileParsers.so.1.2018.09.1 ../../../lib/libRDKitDepictor.so.1.2018.09.1 ../../../lib/libRDKitPartialCharges.so.1.2018.09.1 ../../../lib/libRDKitMolTransforms.so.1.2018.09.1 ../../../lib/libRDKitEigenSolvers.so.1.2018.09.1 ../../../lib/libRDKitFingerprints.so.1.2018.09.1 ../../../lib/libRDKitSubgraphs.so.1.2018.09.1 -lboost_serialization ../../../lib/libRDKitChemTransforms.so.1.2018.09.1 ../../../lib/libRDKitSmilesParse.so.1.2018.09.1 ../../../lib/libRDKitSubstructMatch.so.1.2018.09.1 ../../../lib/libRDKitGraphMol.so.1.2018.09.1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.09.1 ../../../lib/libRDKitDataStructs.so.1.2018.09.1 ../../../lib/libRDKitRDGeneral.so.1.2018.09.1 -lcoordgenlibs -lmaeparser -lpthread make[4]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [100%] Built target molTautomerTest make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[2]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' STATIC_LINK=0 RDKIT_LIBDIR=/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf//lib pg_buildext build /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit build-%v ### build 11 ### make[2]: Entering directory '/build/rdkit-201809.1+dfsg/build-11' gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o rdkit_io.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_io.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o mol_op.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'mol_murckoscaffold': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:253:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] CROMol scaffold = MolMurckoScaffold(mol); ^~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'mol_hash': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:273:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *res = pnstrdup(str, len); ^~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'mol_adjust_query_properties': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:286:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *data = PG_GETARG_CSTRING(1); ^~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:290:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] Mol *res = deconstructROMol(adj); ^~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'mol_to_svg': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:305:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *legend = PG_GETARG_CSTRING(1); ^~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:329:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *res = pnstrdup(str, strlen(str)); ^~~~ In file included from /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:34: /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol2s_transition': /usr/include/postgresql/11/server/fmgr.h:238:29: warning: initialization of 'CROMol' {aka 'void *'} from 'Datum' {aka 'unsigned int'} makes pointer from integer without a cast [-Wint-conversion] #define PG_GETARG_DATUM(n) (fcinfo->arg[n]) ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:381:18: note: in expansion of macro 'PG_GETARG_DATUM' CROMol mol = PG_GETARG_DATUM(1); ^~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:397:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] text *ts = (text *)palloc(ts_size); // new return value ^~~~ In file included from /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:34: /usr/include/postgresql/11/server/fmgr.h:238:29: warning: initialization of 'CROMol' {aka 'void *'} from 'Datum' {aka 'unsigned int'} makes pointer from integer without a cast [-Wint-conversion] #define PG_GETARG_DATUM(n) (fcinfo->arg[n]) ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:409:18: note: in expansion of macro 'PG_GETARG_DATUM' CROMol mol = PG_GETARG_DATUM(1); ^~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:417:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] char *smiles = makeMolText(mol, &len, false); ^~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mols': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:455:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] int32 ts_size = VARHDRSZ + strlen(str); ^~~~~ In file included from /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:34: /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol_transition': /usr/include/postgresql/11/server/fmgr.h:238:29: warning: initialization of 'CROMol' {aka 'void *'} from 'Datum' {aka 'unsigned int'} makes pointer from integer without a cast [-Wint-conversion] #define PG_GETARG_DATUM(n) (fcinfo->arg[n]) ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:477:18: note: in expansion of macro 'PG_GETARG_DATUM' CROMol mol = PG_GETARG_DATUM(1); ^~~~~~~~~~~~~~~ /usr/include/postgresql/11/server/fmgr.h:238:29: warning: initialization of 'CROMol' {aka 'void *'} from 'Datum' {aka 'unsigned int'} makes pointer from integer without a cast [-Wint-conversion] #define PG_GETARG_DATUM(n) (fcinfo->arg[n]) ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:488:18: note: in expansion of macro 'PG_GETARG_DATUM' CROMol mol = PG_GETARG_DATUM(1); ^~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles_transition': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:361:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol_transition': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:496:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o bfp_op.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o sfp_op.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/sfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o rxn_op.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rxn_op.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rxn_op.c:164:1: warning: multi-line comment [-Wcomment] // /* keep compiler quiet - no extra ; */ \ ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rxn_op.c: In function 'reaction_to_svg': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rxn_op.c:179:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] bool highlightByReactants = PG_GETARG_BOOL(1); ^~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o rdkit_gist.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldistsign': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:240:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] uint8 *as = (uint8 *)VARDATA(a); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldist': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:275:16: warning: implicit declaration of function 'floor' [-Wimplicit-function-declaration] return (int) floor(10000*soergeldistsign(a, b)); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:275:16: warning: incompatible implicit declaration of built-in function 'floor' /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:275:16: note: include '' or provide a declaration of 'floor' /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:42:1: +#include /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:275:16: return (int) floor(10000*soergeldistsign(a, b)); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:262:10: warning: unused variable 'd' [-Wunused-variable] double d; ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gmol_consistent': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:526:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] uint8 *k = (uint8 *)VARDATA(key); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:538:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] uint8 *k = (uint8 *)VARDATA(key); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:570:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] uint8 *k = (uint8 *)VARDATA(key); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c: In function 'rdkit_consistent': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:658:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] int siglen = SIGLEN(query); ^~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:673:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] uint8 *k = (uint8 *)VARDATA(key); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gsfp_consistent': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:708:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] int sum, overlapSum, overlapN; ^~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:714:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] int nKey = (ISALLTRUE(key)) ? ^~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c: In function 'greaction_consistent': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:787:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] uint8 *k = (uint8 *)VARDATA(key); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:804:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] uint8 *k = (uint8 *)VARDATA(key); ^~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:832:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] uint8 *k = (uint8 *)VARDATA(key); ^~~~~ At top level: /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:646:1: warning: 'rdkit_consistent' defined but not used [-Wunused-function] rdkit_consistent(GISTENTRY *entry, StrategyNumber strategy, bytea *key, bytea *query) ^~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c:261:1: warning: 'soergeldist' defined but not used [-Wunused-function] soergeldist(bytea *a, bytea *b) { ^~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o bfp_gist.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bfp_gist.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bfp_gist.c: In function 'merge_key': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bfp_gist.c:699:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] int siglen = GBFP_INNER_SIGLEN(result); ^~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o bfp_gin.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bfp_gin.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o low_gist.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/low_gist.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/low_gist.c: In function 'gslfp_consistent': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/low_gist.c:410:30: warning: implicit declaration of function 'searchSfpCache' [-Wimplicit-function-declaration] fcinfo->flinfo->fn_extra = searchSfpCache( ^~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/low_gist.c:410:28: warning: assignment to 'void *' from 'int' makes pointer from integer without a cast [-Wint-conversion] fcinfo->flinfo->fn_extra = searchSfpCache( ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o guc.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/guc.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o cache.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/cache.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/cache.c: In function 'createCache': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/cache.c:312:17: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] methodsOrig = ctx->methods; ^ In file included from /usr/include/postgresql/11/server/postgres.h:47, from /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/cache.c:33: /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/cache.c:341:19: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=] elog(ERROR, "Could not allocate %ld bytes", sizeof(*newholder)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ /usr/include/postgresql/11/server/utils/elog.h:202:23: note: in definition of macro 'elog' elog_finish(elevel, __VA_ARGS__); \ ^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o adapter.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/adapter.cpp gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -fPIC -c -o bitstring.o /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bitstring.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringUnion': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bitstring.c:72:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringIntersection': /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bitstring.c:106:7: warning: unused variable 'i' [-Wunused-variable] int i; ^ g++ -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -shared -o rdkit.so rdkit_io.o mol_op.o bfp_op.o sfp_op.o rxn_op.o rdkit_gist.o bfp_gist.o bfp_gin.o low_gist.o guc.o cache.o adapter.o bitstring.o -L/usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -L/usr/lib/llvm-7/lib -L/usr/lib/arm-linux-gnueabihf/mit-krb5 -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/rdkit-201809.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -L/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf//lib -lRDKitMolDraw2D -lRDKitMolTransforms -lRDKitMolHash -lRDKitFMCS -lRDKitChemReactions -lRDKitChemTransforms -lRDKitFileParsers -lRDKitSmilesParse -lRDKitFingerprints -lRDKitSubgraphs -lRDKitDescriptors -lRDKitPartialCharges -lRDKitSubstructMatch -lRDKitGraphMol -lRDKitEigenSolvers -lRDKitDataStructs -lRDKitDepictor -lRDKitRDGeometryLib -lRDKitRDGeneral -pthread sed -e's/@RDKIT_PG_BFP_GIST_FETCH@/FUNCTION 9 gbfp_fetch (internal),/;' \ -e's/@RDKIT_GIN_BFP_TRICONSISTENT@/FUNCTION 6 gin_bfp_triconsistent(internal, int2, bfp, int4, internal, internal, internal),/' \ -e's/@RDKIT_PARALLEL_SAFE@/PARALLEL SAFE/' \ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit.sql.in > rdkit--3.7.sql /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o rdkit_io.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_io.c /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o mol_op.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:361:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:381:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:409:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:477:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:488:12: warning: incompatible integer to pointer conversion initializing 'CROMol' (aka 'void *') with an expression of type 'Datum' (aka 'unsigned int') [-Wint-conversion] CROMol mol = PG_GETARG_DATUM(1); ^ ~~~~~~~~~~~~~~~~~~ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/mol_op.c:496:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 6 warnings generated. /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o bfp_op.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bfp_op.c /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o sfp_op.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/sfp_op.c /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o rxn_op.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rxn_op.c /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o rdkit_gist.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit_gist.c /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o bfp_gist.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bfp_gist.c /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o bfp_gin.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bfp_gin.c /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o low_gist.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/low_gist.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/low_gist.c:410:30: warning: implicit declaration of function 'searchSfpCache' is invalid in C99 [-Wimplicit-function-declaration] fcinfo->flinfo->fn_extra = searchSfpCache( ^ /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/low_gist.c:410:28: warning: incompatible integer to pointer conversion assigning to 'void *' from 'int' [-Wint-conversion] fcinfo->flinfo->fn_extra = searchSfpCache( ^ ~~~~~~~~~~~~~~~ 2 warnings generated. /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o guc.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/guc.c /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o cache.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/cache.c /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/cache.c:312:17: warning: assigning to 'MemoryContextMethods *' (aka 'struct MemoryContextMethods *') from 'const MemoryContextMethods *' (aka 'const struct MemoryContextMethods *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] methodsOrig = ctx->methods; ^ ~~~~~~~~~~~~ 1 warning generated. /usr/bin/clang-7 -xc++ -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -emit-llvm -c -o adapter.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/adapter.cpp opt-7 -module-summary -f adapter.bc -o adapter.bc /usr/bin/clang-7 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/rdkit-201809.1+dfsg/Code -DRDKITVER='"007300"' -I. -I/build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit -I/usr/include/postgresql/11/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -I/usr/include/mit-krb5 -flto=thin -emit-llvm -c -o bitstring.bc /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/bitstring.c make[2]: Leaving directory '/build/rdkit-201809.1+dfsg/build-11' (cd /build/rdkit-201809.1+dfsg/Code; doxygen doxygen/doxygen.config) warning: Tag `SYMBOL_CACHE_SIZE' at line 337 of file `doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `SHOW_DIRECTORIES' at line 557 of file `doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `HTML_ALIGN_MEMBERS' at line 971 of file `doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `USE_INLINE_TREES' at line 1162 of file `doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `XML_SCHEMA' at line 1425 of file `doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `XML_DTD' at line 1431 of file `doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/tutorial Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/libs Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/QTDemo Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog Searching for files in directory /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog Searching for files in directory 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directory /build/rdkit-201809.1+dfsg/Code/RDGeneral/hash Searching for files in directory /build/rdkit-201809.1+dfsg/Code/RDGeneral/hash/detail Searching for files in directory /build/rdkit-201809.1+dfsg/Code/RDBoost Searching for files in directory /build/rdkit-201809.1+dfsg/Code/DistGeom Searching for files in directory /build/rdkit-201809.1+dfsg/Code/ForceField Searching for files in directory /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF Searching for files in directory /build/rdkit-201809.1+dfsg/Code/ForceField/UFF Searching for files in directory /build/rdkit-201809.1+dfsg/Code/Numerics Searching for files in directory /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment Searching for files in directory /build/rdkit-201809.1+dfsg/Code/Numerics/EigenSolvers Searching for files in directory /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer Searching for files in directory /build/rdkit-201809.1+dfsg/Code/Geometry Searching for files in directory /build/rdkit-201809.1+dfsg/Code/Features Searching for files in directory /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures Reading and parsing tag files Parsing files Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Atom.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/atomic_data.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/atomic_data.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/AtomIterators.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/AtomIterators.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Bond.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Bond.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/BondIterators.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/BondIterators.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Canon.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Canon.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/CartesianProduct.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/RandomSample.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/PreprocessRxn.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/PreprocessRxn.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionFingerprints.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionParser.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionParser.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionPickler.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionPickler.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/MolFragmenter.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Chirality.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Chirality.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Conformer.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/DepictUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/DepictUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/EmbeddedFrag.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/AUTOCORR2D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/AUTOCORR3D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/AUTOCORR3D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/ConnectivityDescriptors.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Crippen.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Crippen.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Data3Ddescriptors.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/EEM.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/EEM.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/GETAWAY.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/GETAWAY.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Lipinski.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Property.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/details.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/details.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Graph.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/RingMatchTableSet.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/RingMatchTableSet.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Seed.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Target.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Target.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/GraphMol.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolBundle.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolBundle.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DQt.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DQt.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MultiMolDraw2D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MultiMolDraw2D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash/MolHash.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/details.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolPickler.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/MonomerInfo.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/MonomerInfo.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/new_canon.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/new_canon.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/PeriodicTable.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/PeriodicTable.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryAtom.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryAtom.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryBond.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryBond.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitBase.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitQueries.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/RDKitQueries.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Resonance.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Resonance.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/RingInfo.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/RingInfo.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Rings.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Rings.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ROMol.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/RWMol.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SanitException.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SanitException.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/primes.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/primes.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StereoGroup.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StereoGroup.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/StructCheckerOptions.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Utilites.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Catalogs/Catalog.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Catalogs/CatalogEntry.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Catalogs/CatalogEntry.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Catalogs/CatalogParams.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Catalogs/CatalogParams.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/base64.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/base64.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/BitOps.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/BitOps.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/BitVect.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/BitVect.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/BitVects.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/BitVects.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/BitVectUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/BitVectUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/DatastructsException.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/DatastructsException.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/DiscreteDistMat.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/DiscreteDistMat.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/DiscreteValueVect.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/DiscreteValueVect.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/ExplicitBitVect.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/ExplicitBitVect.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/FPBReader.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/FPBReader.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/MultiFPBReader.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/SparseBitVect.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/SparseBitVect.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataStructs/SparseIntVect.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataStructs/SparseIntVect.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/AndQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/AndQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/EqualityQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/EqualityQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/GreaterEqualQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/GreaterEqualQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/GreaterQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/GreaterQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/LessEqualQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/LessEqualQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/LessQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/LessQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/OrQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/OrQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/Query.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/Query.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/QueryObjects.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/RangeQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/RangeQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/SetQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/SetQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Query/XOrQuery.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Query/XOrQuery.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/CorrMatGenerator.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/CorrMatGenerator.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoBitRanker.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoBitRanker.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoGainFuncs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/InfoGainFuncs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/SimDivPickers/DistPicker.h... Parsing file /build/rdkit-201809.1+dfsg/Code/SimDivPickers/DistPicker.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /build/rdkit-201809.1+dfsg/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/SimDivPickers/MaxMinPicker.h... Parsing file /build/rdkit-201809.1+dfsg/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/BadFileException.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/BoostEndInclude.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/BoostEndInclude.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/BoostStartInclude.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/BoostStartInclude.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/Dict.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/Exceptions.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/Exceptions.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/export.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/export.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/FileParseException.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/FileParseException.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/hanoiSort.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/hanoiSort.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/Invariant.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/LocaleSwitcher.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/Ranking.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/Ranking.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDAny.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDAny.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDConfig.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDConfig.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDLog.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDProps.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDProps.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDThreads.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDThreads.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/RDValue.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/StreamOps.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/StreamOps.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/types.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/utils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDGeneral/versions.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDGeneral/versions.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDBoost/boost_numpy.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDBoost/boost_numpy.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDBoost/import_array.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDBoost/import_array.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDBoost/iterator_next.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDBoost/iterator_next.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDBoost/pyint_api.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDBoost/pyint_api.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDBoost/PySequenceHolder.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDBoost/python.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h... Parsing file /build/rdkit-201809.1+dfsg/Code/RDBoost/python_streambuf.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DistGeom/BoundsMatrix.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DistGeom/BoundsMatrix.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DistGeom/ChiralSet.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DistGeom/ChiralSet.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DistGeom/ChiralViolationContrib.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DistGeom/ChiralViolationContrib.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DistGeom/DistGeomUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DistGeom/DistGeomUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DistGeom/DistViolationContrib.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DistGeom/DistViolationContrib.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DistGeom/FourthDimContrib.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DistGeom/FourthDimContrib.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/DistGeom/TriangleSmooth.h... Parsing file /build/rdkit-201809.1+dfsg/Code/DistGeom/TriangleSmooth.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/Contrib.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/Contrib.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/ForceField.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/ForceField.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleBend.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleBend.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleConstraint.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleConstraint.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/BondStretch.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/BondStretch.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Contribs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Contribs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/DistanceConstraint.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Nonbonded.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/OopBend.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/OopBend.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleBend.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/BondStretch.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Contribs.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Contribs.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Inversion.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Inversion.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Forc/build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Contribs.h:15: warning: the name `Contribs.h' supplied as the second argument in the \file statement matches the following input files: /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Contribs.h /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Contribs.h Please use a more specific name by including a (larger) part of the path! /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Contribs.h:13: warning: the name `Contribs.h' supplied as the second argument in the \file statement matches the following input files: /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Contribs.h /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Contribs.h Please use a more specific name by including a (larger) part of the path! eField/UFF/Nonbonded.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Params.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Params.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Numerics/Matrix.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Numerics/Matrix.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Numerics/SquareMatrix.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Numerics/SquareMatrix.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Numerics/SymmMatrix.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Numerics/SymmMatrix.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Numerics/Vector.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Numerics/Vector.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Geometry/Grid3D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Geometry/Grid3D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Geometry/GridUtils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Geometry/GridUtils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Geometry/point.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Geometry/point.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Geometry/Transform.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Geometry/Transform.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Geometry/Transform2D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Geometry/Transform2D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Geometry/Transform3D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Geometry/Transform3D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Geometry/UniformGrid3D.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Geometry/UniformGrid3D.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Geometry/Utils.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Geometry/Utils.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/Features/Feature.h... Parsing file /build/rdkit-201809.1+dfsg/Code/Features/Feature.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/FreeChemicalFeature.h... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree 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... Computing dependencies between directories... Generating citations page... 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... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file AcidBaseCatalogEntry.h... Generating code for file AcidBaseCatalogParams.h... Generating code for file AcidBaseCatalogUtils.h... Generating code for file AlignMolecules.h... Generating code for file AlignPoints.h... Generating code for file AndQuery.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 Atom.h... Generating code for file atomic_data.h... Generating code for file AtomIterators.h... Generating code for file AtomPairGenerator.h... Generating code for file AtomPairs.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file AUTOCORR2D.h... Generating code for file AUTOCORR3D.h... Generating code for file BadFileException.h... Generating code for file base64.h... Generating code for file BFGSOpt.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 Bond.h... Generating code for file BondIterators.h... Generating code for file BondStretch.h... Generating code for file BondStretch.h... Generating code for file boost_numpy.h... Generating code for file BoostEndInclude.h... Generating code for file BoostStartInclude.h... Generating code for file BoundsMatrix.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Builder.h... Generating code for file Builder.h... Generating code for file Canon.h... Generating code for file CartesianProduct.h... Generating code for file Catalog.h... Generating code for file CatalogEntry.h... Generating code for file CatalogParams.h... Generating code for file Charge.h... Generating code for file ChemicalFeature.h... Generating code for file ChemTransforms.h... Generating code for file Chirality.h... Generating code for file ChiralSet.h... Generating code for file ChiralViolationContrib.h... Generating code for file Composition2N.h... Generating code for file Conformer.h... Generating code for file ConnectivityDescriptors.h... Generating code for file Contrib.h... Generating code for file Contribs.h... Generating code for file Contribs.h... Generating code for file CorrMatGenerator.h... Generating code for file Crippen.h... Generating code for file Data3Ddescriptors.h... Generating code for file DatastructsException.h... Generating code for file DebugTrace.h... Generating code for file DepictUtils.h... Generating code for file details.h... Generating code for file details.h... Generating code for file Dict.h... Generating code for file DiscreteDistMat.h... Generating code for file DiscreteValueVect.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file DistGeomUtils.h... Generating code for file DistPicker.h... Generating code for file DistViolationContrib.h... Generating code for file DuplicatedSeedCache.h... Generating code for file EEM.h... Generating code for file EmbeddedFrag.h... Generating code for file Embedder.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 EqualityQuery.h... Generating code for file EvenSamplePairs.h... Generating code for file Exceptions.h... Generating code for file ExplicitBitVect.h... Generating code for file export.h... Generating code for file Feature.h... Generating code for file FeatureParser.h... Generating code for file FileParseException.h... Generating code for file FileParsers.h... Generating code for file FileParserUtils.h... Generating code for file FilterCatalog.h... Generating code for file FilterCatalogEntry.h... Generating code for file FilterMatcherBase.h... Generating code for file FilterMatchers.h... Generating code for file Filters.h... Generating code for file FingerprintGenerator.h... Generating code for file Fingerprints.h... Generating code for file FingerprintUtil.h... Generating code for file FMCS.h... Generating code for file ForceField.h... Generating code for file FourthDimContrib.h... Generating code for file FPBReader.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... Generating code for file FragCatGenerator.h... Generating code for file FragCatParams.h... Generating code for file FragFPGenerator.h... Generating code for file Fragment.h... Generating code for file FragmentCatalogEntry.h... Generating code for file FragmentCatalogParams.h... Generating code for file FragmentCatalogUtils.h... Generating code for file FreeChemicalFeature.h... Generating code for file FunctionalGroupHierarchy.h... Generating code for file GasteigerCharges.h... Generating code for file GasteigerParams.h... Generating code for file GETAWAY.h... Generating code for file Graph.h... Generating code for file GraphMol.h... Generating code for file GreaterEqualQuery.h... Generating code for file GreaterQuery.h... Generating code for file Grid3D.h... Generating code for file GridUtils.h... Generating code for file hanoiSort.h... Generating code for file HierarchicalClusterPicker.h... Generating code for file import_array.h... Generating code for file InfoBitRanker.h... Generating code for file InfoGainFuncs.h... Generating code for file Invariant.h... Generating code for file Inversion.h... Generating code for file iterator_next.h... Generating code for file LessEqualQuery.h... Generating code for file LessQuery.h... Generating code for file Lipinski.h... Generating code for file LocaleSwitcher.h... Generating code for file MACCS.h... Generating code for file MatchTable.h... Generating code for file Matrix.h... Generating code for file MaximumCommonSubgraph.h... Generating code for file MaxMinPicker.h... Generating code for file Metal.h... Generating code for file MetricFuncs.h... Generating code for file MetricMatrixCalc.h... Generating code for file MMFF.h... Generating code for file MMPA.h... Generating code for file MolBundle.h... Generating code for file MolCatalog.h... Generating code for file MolCatalogEntry.h... Generating code for file MolCatalogParams.h... Generating code for file MolChemicalFeature.h... Generating code for file MolChemicalFeatureDef.h... Generating code for file MolChemicalFeatureFactory.h... Generating code for file MolData3Ddescriptors.h... Generating code for file MolDescriptors.h... Generating code for file MolDescriptors3D.h... Generating code for file MolDraw2D.h... Generating code for file MolDraw2DCairo.h... Generating code for file MolDraw2DDetails.h... Generating code for file MolDraw2DQt.h... Generating code for file MolDraw2DSVG.h... Generating code for file MolDraw2DUtils.h... Generating code for file MolDraw2Dwx.h... Generating code for file MolFileStereochem.h... Generating code for file MolFragmenter.h... Generating code for file MolHash.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... Generating code for file MolStandardize.h... Generating code for file MolSupplier.h... Generating code for file MolSurf.h... Generating code for file MolTransforms.h... Generating code for file MolWriters.h... Generating code for file MonomerInfo.h... Generating code for file MorganFingerprints.h... Generating code for file MorganGenerator.h... Generating code for file MORSE.h... Generating code for file MQN.h... Generating code for file MultiFPBReader.h... Generating code for file MultiMolDraw2D.h... Generating code for file new_canon.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... Generating code for file Normalize.h... Generating code for file O3AAlignMolecules.h... Generating code for file OopBend.h... Generating code for file OrQuery.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file Pattern.h... Generating code for file PBF.h... Generating code for file PeriodicTable.h... Generating code for file PMI.h... Generating code for file point.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PowerEigenSolver.h... Generating code for file PreprocessRxn.h... Generating code for file primes.h... Generating code for file Property.h... Generating code for file ProximityBonds.h... Generating code for file pyint_api.h... Generating code for file PySequenceHolder.h... Generating code for file python.h... Generating code for file python_streambuf.h... Generating code for file Query.h... Generating code for file QueryAtom.h... Generating code for file QueryBond.h... Generating code for file QueryObjects.h... Generating code for file QueryOps.h... Generating code for file RandomSample.h... Generating code for file RandomSampleAllBBs.h... Generating code for file RangeQuery.h... Generating code for file Ranking.h... Generating code for file RDAny.h... Generating code for file RDConfig.h... Generating code for file RDDepictor.h... Generating code for file RDF.h... Generating code for file RDKitBase.h... Generating code for file RDKitFPGenerator.h... Generating code for file RDKitQueries.h... Generating code for file RDLog.h... Generating code for file RDProps.h... Generating code for file RDThreads.h... Generating code for file RDValue-doublemagic.h... Generating code for file RDValue-taggedunion.h... Generating code for file RDValue.h... Generating code for file 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 ReCharge.h... Generating code for file ReducedGraphs.h... Generating code for file RegisterDescriptor.h... Generating code for file Resonance.h... Generating code for file RGroupDecomp.h... Generating code for file RingInfo.h... Generating code for file RingMatchTableSet.h... Generating code for file Rings.h... Generating code for file ROMol.h... Generating code for file RWMol.h... Generating code for file SanitException.h... Generating code for file SanitizeRxn.h... Generating code for file Seed.h... Generating code for file SeedSet.h... Generating code for file SequenceParsers.h... Generating code for file SequenceWriters.h... Generating code for file SetQuery.h... Generating code for file ShapeEncoder.h... Generating code for file ShapeUtils.h... Generating code for file SLNAttribs.h... Generating code for file SLNParse.h... Generating code for file SLNParseOps.h... Generating code for file SmartsWrite.h... Generating code for file SmilesParse.h... Generating code for file SmilesParseOps.h... Generating code for file SmilesWrite.h... Generating code for file Snapshot.h... Generating code for file SparseBitVect.h... Generating code for file SparseIntVect.h... Generating code for file SquareMatrix.h... Generating code for file Stereo.h... Generating code for file StereoGroup.h... Generating code for file StreamOps.h... Generating code for file StretchBend.h... Generating code for file StripSmallFragments.h... Generating code/build/rdkit-201809.1+dfsg/Code/DataStructs/BitOps.h:174: warning: found at different nesting level (7) than expected (4) /build/rdkit-201809.1+dfsg/Code/DataStructs/BitOps.h:175: warning: end of comment block while expecting command for file StructChecker.h... Generating code for file StructCheckerOptions.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... Generating code for file SubstructLibrary.h... Generating code for file SubstructMatch.h... Generating code for file SubstructMatchCustom.h... Generating code for file SubstructureCache.h... Generating code for file SubstructUtils.h... Generating code for file SymmMatrix.h... Generating code for file Target.h... Generating code for file TargetMatch.h... Generating code for file Tautomer.h... Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... Generating code for file TopologicalTorsionGenerator.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngleM6.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionPreferences.h... Generating code for file Trajectory.h... Generating code for file Transform.h... Generating code for file Transform2D.h... Generating code for file Transform3D.h... Generating code for file TransformCatalogEntry.h... Generating code for file TransformCatalogParams.h... Generating code for file TransformCatalogUtils.h... Generating code for file TriangleSmooth.h... Generating code for file types.h... Generating code for file UFF.h... Generating code for file UniformGrid3D.h... Generating code for file USRDescriptor.h... Generating code for file Utilites.h... Generating code for file Utils.h... Generating code for file utils.h... Generating code for file Validate.h... Generating code for file Vector.h... Generating code for file versions.h... Generating code for file WHIM.h... Generating code for file XOrQuery.h... Generating file documentation... Generating docs for file AcidBaseCatalogEntry.h... Generating docs for file AcidBaseCatalogParams.h... Generating docs for file AcidBaseCatalogUtils.h... Generating docs for file AlignMolecules.h... Generating docs for file AlignPoints.h... Generating docs for file AndQuery.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraint.h... Generating docs for file Atom.h... Generating docs for file atomic_data.h... Generating docs for file AtomIterators.h... Generating docs for file AtomPairGenerator.h... Generating docs for file AtomPairs.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file AUTOCORR2D.h... Generating docs for file AUTOCORR3D.h... Generating docs for file BadFileException.h... Generating docs for file base64.h... Generating docs for file BFGSOpt.h... Generating docs for file BitOps.h... Generating docs for file BitVect.h... Generating docs for file BitVects.h... Generating docs for file BitVectUtils.h... Generating docs for file Bond.h... Generating docs for file BondIterators.h... Generating docs for file BondStretch.h... Generating docs for file BondStretch.h... Generating docs for file boost_numpy.h... Generating docs for file BoostEndInclude.h... Generating docs for file BoostStartInclude.h... Generating docs for file BoundsMatrix.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Builder.h... Generating docs for file Builder.h... Generating docs for file Canon.h... Generating docs for file CartesianProduct.h... Generating docs for file Catalog.h... Generating docs for file CatalogEntry.h... Generating docs for file CatalogParams.h... Generating docs for file Charge.h... Generating docs for file ChemicalFeature.h... Generating docs for file ChemTransforms.h... Generating docs for file Chirality.h... Generating docs for file ChiralSet.h... Generating docs for file ChiralViolationContrib.h... Generating docs for file Composition2N.h... Generating docs for file Conformer.h... Generating docs for file ConnectivityDescriptors.h... Generating docs for file Contrib.h... Generating docs for file Contribs.h... Generating docs for file Contribs.h... Generating docs for file CorrMatGenerator.h... Generating docs for file Crippen.h... Generating docs for file Data3Ddescriptors.h... Generating docs for file DatastructsException.h... Generating docs for file DebugTrace.h... Generating docs for file DepictUtils.h... Generating docs for file details.h... Generating docs for file details.h... Generating docs for file Dict.h... Generating docs for file DiscreteDistMat.h... Generating docs for file DiscreteValueVect.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistGeomUtils.h... Generating docs for file DistPicker.h... Generating docs for file DistViolationContrib.h... Generating docs for file DuplicatedSeedCache.h... Generating docs for file EEM.h... Generating docs for file EmbeddedFrag.h... Generating docs for file Embedder.h... Generating docs for file Enumerate.h... Generating docs for file EnumerateBase.h... Generating docs for file EnumerateTypes.h... Generating docs for file EnumerationPickler.h... Generating docs for file EnumerationStrategyBase.h... Generating docs for file EqualityQuery.h... Generating docs for file EvenSamplePairs.h... Generating docs for file Exceptions.h... Generating docs for file ExplicitBitVect.h... Generating docs for file export.h... Generating docs for file Feature.h... Generating docs for file FeatureParser.h... Generating docs for file FileParseException.h... Generating docs for file FileParsers.h... Generating docs for file FileParserUtils.h... Generating docs for file FilterCatalog.h... Generating docs for file FilterCatalogEntry.h... Generating docs for file FilterMatcherBase.h... Generating docs for file FilterMatchers.h... Generating docs for file Filters.h... Generating docs for file FingerprintGenerator.h... Generating docs for file Fingerprints.h... Generating docs for file FingerprintUtil.h... Generating docs for file FMCS.h... Generating docs for file ForceField.h... Generating docs for file FourthDimContrib.h... Generating docs for file FPBReader.h... Generating docs for file FragCatalogEntry.h... Generating docs for file FragCatalogUtils.h... Generating docs for file FragCatGenerator.h... Generating docs for file FragCatParams.h... Generating docs for file FragFPGenerator.h... Generating docs for file Fragment.h... Generating docs for file FragmentCatalogEntry.h... Generating docs for file FragmentCatalogParams.h... Generating docs for file FragmentCatalogUtils.h... Generating docs for file FreeChemicalFeature.h... Generating docs for file FunctionalGroupHierarchy.h... Generating docs for file GasteigerCharges.h... Generating docs for file GasteigerParams.h... Generating docs for file GETAWAY.h... Generating docs for file Graph.h... Generating docs for file GraphMol.h... Generating docs for file GreaterEqualQuery.h... Generating docs for file GreaterQuery.h... Generating docs for file Grid3D.h... Generating docs for file GridUtils.h... Generating docs for file hanoiSort.h... Generating docs for file HierarchicalClusterPicker.h... Generating docs for file import_array.h... Generating docs for file InfoBitRanker.h... Generating docs for file InfoGainFuncs.h... Generating docs for file Invariant.h... Generating docs for file Inversion.h... Generating docs for file iterator_next.h... Generating docs for file LessEqualQuery.h... Generating docs for file LessQuery.h... Generating docs for file Lipinski.h... Generating docs for file LocaleSwitcher.h... Generating docs for file MACCS.h... Generating docs for file MatchTable.h... Generating docs for file Matrix.h... Generating docs for file MaximumCommonSubgraph.h... Generating docs for file MaxMinPicker.h... Generating docs for file Metal.h... Generating docs for file MetricFuncs.h... Generating docs for file MetricMatrixCalc.h... Generating docs for file MMFF.h... Generating docs for file MMPA.h... Generating docs for file MolBundle.h... Generating docs for file/build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:485: warning: Found unknown command `\overloadquery' /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:494: warning: Found unknown command `\overloadquery' MolCatalog.h... Generating docs for file MolCatalogEntry.h... Generating docs for file MolCatalogParams.h... Generating docs for file MolChemicalFeature.h... Generating docs for file MolChemicalFeatureDef.h... Generating docs for file MolChemicalFeatureFactory.h... Generating docs for file MolData3Ddescriptors.h... Generating docs for file MolDescriptors.h... Generating docs for file MolDescriptors3D.h... Generating docs for file MolDraw2D.h... Generating docs for file MolDraw2DCairo.h... Generating docs for file MolDraw2DDetails.h... Generating docs for file MolDraw2DQt.h... Generating docs for file MolDraw2DSVG.h... Generating docs for file MolDraw2DUtils.h... Generating docs for file MolDraw2Dwx.h... Generating docs for file MolFileStereochem.h... Generating docs for file MolFragmenter.h... Generating docs for file MolHash.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... Generating docs for file MolStandardize.h... Generating docs for file MolSupplier.h... Generating docs for file MolSurf.h... Generating docs for file MolTransforms.h... Generating docs for file MolWriters.h... Generating docs for file MonomerInfo.h... Generating docs for file MorganFingerprints.h... Generating docs for file MorganGenerator.h... Generating docs for file MORSE.h... Generating docs for file MQN.h... Generating docs for file MultiFPBReader.h... Generating docs for file MultiMolDraw2D.h... Generating docs for file new_canon.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... Generating docs for file Normalize.h... Generating docs for file O3AAlignMolecules.h... Generating docs for file OopBend.h... Generating docs for file OrQuery.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file Pattern.h... Generating docs for file PBF.h... Generating docs for file PeriodicTable.h... Generating docs for file PMI.h... Generating docs for file point.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file PowerEigenSolver.h... Generating docs for file PreprocessRxn.h... Generating docs for file primes.h... Generating docs for file Property.h... Generating docs for file ProximityBonds.h... Generating docs for file pyint_api.h... Generating docs for file PySequenceHolder.h... Generating docs for file python.h... Generating docs for file python_streambuf.h... Generating docs for file Query.h... Generating docs for file QueryAtom.h... Generating docs for file QueryBond.h... Generating docs for file QueryObjects.h... Generating docs for file QueryOps.h... Generating docs for file RandomSample.h... Generating docs for file RandomSampleAllBBs.h... Generating docs for file RangeQuery.h... Generating docs for file Ranking.h... Generating docs for file RDAny.h... Generating docs for file RDConfig.h... Generating docs for file RDDepictor.h... Generating docs for file RDF.h... Generating docs for file RDKitBase.h... Generating docs for file RDKitFPGenerator.h... Generating docs for file RDKitQueries.h... Generating docs for file RDLog.h... Generating docs for file RDProps.h... Generating docs for file RDThreads.h... Generating docs for file RDValue-doublemagic.h... Generating docs for file RDValue-taggedunion.h... Generating docs for file RDValue.h... Generating docs for file Reaction.h... Generating docs for file ReactionFingerprints.h... Generating docs for file ReactionParser.h... Generating docs for file ReactionPickler.h... Generating docs for file ReactionRunner.h... Generating docs for file ReactionUtils.h... Generating docs for file ReCharge.h... Generating docs for file ReducedGraphs.h... Generating docs for file RegisterDescriptor.h... Generating docs for file Resonance.h... Generating docs for file RGroupDecomp.h... Generating docs for file RingInfo.h... Generating docs for file RingMatchTableSet.h... Generating docs for file Rings.h... Generating docs for file ROMol.h... Generating docs for file RWMol.h... Generating docs for file SanitException.h... Generating docs for file SanitizeRxn.h... Generating docs for file Seed.h... Generating docs for file SeedSet.h... Generating docs for file SequenceParsers.h... Generating docs for file SequenceWriters.h... Generating docs for file SetQuery.h... Generating docs for file ShapeEncoder.h... Generating docs for file ShapeUtils.h... Generating docs for file SLNAttribs.h... Generating docs for file SLNParse.h... Generating docs for file SLNParseOps.h... Generating docs for file SmartsWrite.h... Generating docs for file SmilesParse.h... Generating docs for file SmilesParseOps.h... Generating docs for file SmilesWrite.h... Generating docs for file Snapshot.h... Generating docs for file SparseBitVect.h... Generating docs for file SparseIntVect.h... Generating docs for file SquareMatrix.h... Generating docs for file Stereo.h... Generating docs for file StereoGroup.h... Generating docs for file StreamOps.h... Generating docs for file StretchBend.h... Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... Generating docs for file SubstructLibrary.h... Generating docs for file SubstructMatch.h... Generating docs for file SubstructMatchCustom.h... Generating docs for file SubstructureCache.h... Generating docs for file SubstructUtils.h... Generating docs for file SymmMatrix.h... Generating docs for file Target.h... Generating docs for file TargetMatch.h... Generating docs for file Tautomer.h... Generating docs for file Tautomer.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... Generating docs for file TopologicalTorsionGenerator.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionPreferences.h... Generating docs for file Trajectory.h... Generating docs for file Transform.h... Generating docs for file Transform2D.h... Generating docs for file Transform3D.h... Generating docs for file TransformCatalogEntry.h... Generating docs for file TransformCatalogParams.h... Generating docs for file TransformCatalogUtils.h... Generating docs for file TriangleSmooth.h... Generating docs for file types.h... Generating docs for file UFF.h... Generating docs for file UniformGrid3D.h... Generating docs for file USRDescriptor.h... Generating docs for file Utilites.h... Generating docs for file Utils.h... Generating docs for file utils.h... Generating docs for file Validate.h... Generating docs for file Vector.h... Generating docs for file versions.h... Generating docs for file WHIM.h... Generating docs for file XOrQuery.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound BitVect... Generating docs for compound Data3Ddescriptors... Generating docs for compound DatastructsException... Generating docs for compound ExplicitBitVect... Generating docs for compound IndexErrorException... Generating docs for compound KeyErrorException... Generating docs for compound MolData3Ddescriptors... Generating docs for compound PySequenceHolder... Generating docs for compound SparseBitVect... Generating docs for compound ValueErrorException... Generating namespace index... Generating docs for namespace BFGSOpt Generating docs for namespace boost Generating docs for namespace boost::logging Generating docs for compound boost::logging::rdLogger... Generating docs for namespace boost_adaptbx Generating docs for namespace boost_adaptbx::python Generating docs for compound boost_adaptbx::python::ostream... Generating docs for compound boost_adaptbx::python::streambuf... Generating docs for nested compound boost_adaptbx::python::streambuf::istream... Generating docs for nested compo/build/rdkit-201809.1+dfsg/Code/ForceField/ForceField.h:133: 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/rdkit-201809.1+dfsg/Code/ForceField/ForceField.h:139: 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/rdkit-201809.1+dfsg/Code/ForceField/ForceField.h:139: 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/rdkit-201809.1+dfsg/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/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleBend.h:40: 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/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleConstraint.h:27: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleConstraint.h:27: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/AngleConstraint.h:36: warning: The following parameters of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/rdkit-201809.1+dfsg/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/rdkit-201809.1+dfsg/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/rdkit-201809.1+dfsg/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/rdkit-201809.1+dfsg/Code/ForceField/MMFF/BondStretch.h:36: warning: The following parameters of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) are not documented: parameter 'mmffBondParams' /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Nonbonded.h:59: warning: The following parameters of ForceFields::MMFF::EleContrib::EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, double chargeTerm, boost::uint8_t dielModel, bool is1_4) are not documented: parameter 'chargeTerm' parameter 'dielModel' parameter 'is1_4' /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.h:161: warning: argument 'mmffArom' of command @param is not found in the argument list of ForceFields::MMFF::MMFFAromCollection::getMMFFArom(const boost::uint8_t *aromatic_types=NULL) /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.h:177: warning: The following parameters of ForceFields::MMFF::MMFFAromCollection::getMMFFArom(const boost::uint8_t *aromatic_types=NULL) are not documented: parameter 'aromatic_types' /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.h:1086: warning: The following parameters of ForceFields::MMFF::MMFFOopCollection::getMMFFOop(const bool isMMFFs=false, const std::string &mmffOop="") are not documented: parameter 'isMMFFs' /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Params.h:1215: warning: The following parameters of ForceFields::MMFF::MMFFTorCollection::getMMFFTor(const bool isMMFFs, const std::string &mmffTor="") are not documented: parameter 'isMMFFs' /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/PositionConstraint.h:28: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::MMFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/rdkit-201809.1+dfsg/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/rdkit-201809.1+dfsg/Code/ForceField/MMFF/StretchBend.h:41: 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/rdkit-201809.1+dfsg/Code/ForceField/MMFF/TorsionAngle.h:34: 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/rdkit-201809.1+dfsg/Code/ForceField/MMFF/TorsionAngle.h:45: warning: The following parameters of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) are not documented: parameter 'mmffTorParams' /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF/Nonbonded.h:35: warning: The following parameters of ForceFields::MMFF::VdWContrib::VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants) are not documented: parameter 'mmffVdWConstants' /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleConstraint.h:27: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleConstraint.h:27: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/AngleConstraint.h:36: warning: The following parameters of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' und boost_adaptbx::python::streambuf::ostream... Generating docs for compound boost_adaptbx::python::streambuf_capsule... Generating docs for namespace ChemicalFeatures Generating docs for compound ChemicalFeatures::ChemicalFeature... Generating docs for compound ChemicalFeatures::FreeChemicalFeature... Generating docs for namespace DistGeom Generating docs for compound DistGeom::BoundsMatrix... Generating docs for compound DistGeom::ChiralSet... Generating docs for compound DistGeom::ChiralViolationContrib... Generating docs for compound DistGeom::DistViolationContrib... Generating docs for compound DistGeom::FourthDimContrib... Generating docs for namespace ForceFields Generating docs for compound ForceFields::ForceField... Generating docs for compound ForceFields::ForceFieldContrib... Generating docs for namespace ForceFields::CrystalFF Generating docs for compound ForceFields::CrystalFF::TorsionAngleContribM6... Generating docs for namespace ForceFields::MMFF Generating docs for compound ForceFields::MMFF::AngleBendContrib... Generating docs for compound ForceFields::MMFF::AngleConstraintContrib... Generating docs for compound ForceFields::MMFF::BondStretchContrib... Generating docs for compound ForceFields::MMFF::DistanceConstraintContrib... Generating docs for compound ForceFields::MMFF::EleContrib... Generating docs for compound ForceFields::MMFF::MMFFAngle... Generating docs for compound ForceFields::MMFF::MMFFAngleCollection... Generating docs for compound ForceFields::MMFF::MMFFAromCollection... Generating docs for compound ForceFields::MMFF::MMFFBndkCollection... Generating docs for compound ForceFields::MMFF::MMFFBond... Generating docs for compound ForceFields::MMFF::MMFFBondCollection... Generating docs for compound ForceFields::MMFF::MMFFChg... Generating docs for compound ForceFields::MMFF::MMFFChgCollection... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEle... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEleCollection... Generating docs for compound ForceFields::MMFF::MMFFDef... Generating docs for compound ForceFields::MMFF::MMFFDefCollection... Generating docs for compound ForceFields::MMFF::MMFFDfsbCollection... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurie... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurieCollection... Generating docs for compound ForceFields::MMFF::MMFFOop... Generating docs for compound ForceFields::MMFF::MMFFOopCollection... Generating docs for compound ForceFields::MMFF::MMFFPBCI... Generating docs for compound ForceFields::MMFF::MMFFPBCICollection... Generating docs for compound ForceFields::MMFF::MMFFProp... Generating docs for compound ForceFields::MMFF::MMFFPropCollection... Generating docs for compound ForceFields::MMFF::MMFFStbn... Generating docs for compound ForceFields::MMFF::MMFFStbnCollection... Generating docs for compound ForceFields::MMFF::MMFFTor... Generating docs for compound ForceFields::MMFF::MMFFTorCollection... Generating docs for compound ForceFields::MMFF::MMFFVdW... Generating docs for compound ForceFields::MMFF::MMFFVdWCollection... Generating docs for compound ForceFields::MMFF::MMFFVdWRijstarEps... Generating docs for compound ForceFields::MMFF::OopBendContrib... Generating docs for compound ForceFields::MMFF::PositionConstraintContrib... Generating docs for compound ForceFields::MMFF::StretchBendContrib... Generating docs for compound ForceFields::MMFF::TorsionAngleContrib... Generating docs for compound ForceFields::MMFF::TorsionConstraintContrib... Generating docs for compound ForceFields::MMFF::VdWContrib... Generating docs for namespace ForceFields::MMFF::Utils Generating docs for namespace ForceFields::UFF Generating docs for compound ForceFields::UFF::AngleBendContrib... Generating docs for compound ForceFields::UFF::AngleConstraintContrib... Generating docs for compound ForceFields::UFF::AtomicParams... Generating docs for compound ForceFields::UFF::BondStretchContrib... Generating docs for compound ForceFields::UFF::DistanceConstraintContrib... Generating docs for comp/build/rdkit-201809.1+dfsg/Code/ForceField/UFF/Inversion.h:39: warning: The following parameters 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) are not documented: parameter 'oobForceScalingFactor' /build/rdkit-201809.1+dfsg/Code/ForceField/UFF/PositionConstraint.h:28: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::UFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h:73: warning: The following parameters of RDDepict::compute2DCoords(RDKit::ROMol &mol, const RDGeom::INT_POINT2D_MAP *coordMap=0, bool canonOrient=false, bool clearConfs=true, unsigned int nFlipsPerSample=0, unsigned int nSamples=0, int sampleSeed=0, bool permuteDeg4Nodes=false, bool forceRDKit=false) are not documented: parameter 'forceRDKit' /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h:130: warning: The following parameters of RDDepict::compute2DCoordsMimicDistMat(RDKit::ROMol &mol, const DOUBLE_SMART_PTR *dmat=0, bool canonOrient=true, bool clearConfs=true, double weightDistMat=0.5, unsigned int nFlipsPerSample=3, unsigned int nSamples=100, int sampleSeed=25, bool permuteDeg4Nodes=true, bool forceRDKit=false) are not documented: parameter 'forceRDKit' /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h:162: warning: The following parameters of RDDepict::generateDepictionMatching2DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=static_cast< RDKit::ROMol * >(0), bool acceptFailure=false, bool forceRDKit=false) are not documented: parameter 'forceRDKit' /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h:170: 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=0, bool acceptFailure=false, bool forceRDKit=false) /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/RDDepictor.h:189: warning: The following parameters of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=0, bool acceptFailure=false, bool forceRDKit=false) are not documented: parameter 'referencePattern' parameter 'forceRDKit' /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:485: warning: Found unknown command `\overloadquery' /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:494: warning: Found unknown command `\overloadquery' /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceParsers.h:94: warning: argument 'seq' of command @param is not found in the argument list of RDKit::HELMToMol(const char *helm, bool sanitize=true) /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/SequenceParsers.h:99: warning: The following parameters of RDKit::HELMToMol(const char *helm, bool sanitize=true) are not documented: parameter 'helm' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h:105: warning: The following parameters 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=0, ExplicitBitVect *setOnlyBits=0, bool branchedPaths=true, const std::vector< boost::uint32_t > *fromAtoms=0) are not documented: parameter 'fromAtoms' /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:485: warning: Found unknown command `\overloadquery' /build/rdkit-201809.1+dfsg/Code/GraphMol/QueryOps.h:494: warning: Found unknown command `\overloadquery' /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:267: 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/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/FileParsers.h:278: warning: The following parameters of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) are not documented: parameter 'fname' /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse/SmilesWrite.h:71: warning: The following parameters of RDKit::MolToSmiles(const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) are not documented: parameter 'doRandom' /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:236: warning: argument 'delimiter' of command @param is not found in the argument list of RDKit::parseQueryDefFile(const std::string &filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true) /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:236: warning: argument 'comment' of command @param is not found in the argument list of RDKit::parseQueryDefFile(const std::string &filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true) /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:236: warning: argument 'nameColumn' of command @param is not found in the argument list of RDKit::parseQueryDefFile(const std::string &filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true) /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:236: warning: argument 'smartsColumn' of command @param is not found in the argument list of RDKit::parseQueryDefFile(const std::string &filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h:26: 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< boost::uint32_t > *atomInvariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, std::vector< std::vector< boost::uint32_t > > *atomBits=0, std::map< boost::uint32_t, std::vector< std::vector< int > > > *bitInfo=0) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Fingerprints.h:53: 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< boost::uint32_t > *atomInvariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, std::vector< std::vector< boost::uint32_t > > *atomBits=0, std::map< boost::uint32_t, std::vector< std::vector< int > > > *bitInfo=0) are not documented: parameter 'useBondOrder' parameter 'bitInfo' /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h:96: warning: The following parameters of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) are not documented: parameter 'product' /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms/ChemTransforms.h:111: 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/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h:64: 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/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/ReactionRunner.h:77: 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/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintGenerator.h:107: warning: The following parameters of RDKit::AtomEnvironment::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const=0 are not documented: parameter 'AdditionalOutput' ound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::PositionConstraintContrib... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::TorsionConstraintContrib... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for namespace ForceFields::UFF::Params Generating docs for namespace ForceFields::UFF::Utils Generating docs for namespace Invar Generating docs for compound Invar::Invariant... Generating docs for namespace MolTransforms Generating docs for namespace Queries Generating docs for compound Queries::AndQuery... Generating docs for compound Queries::EqualityQuery... Generating docs for compound Queries::GreaterEqualQuery... Generating docs for compound Queries::GreaterQuery... Generating docs for compound Queries::Int2Type... Generating docs for compound Queries::LessEqualQuery... Generating docs for compound Queries::LessQuery... Generating docs for compound Queries::OrQuery... Generating docs for compound Queries::Query... Generating docs for compound Queries::RangeQuery... Generating docs for compound Queries::SetQuery... Generating docs for compound Queries::XOrQuery... Generating docs for namespace Rankers Generating docs for compound Rankers::argless... Generating docs for compound Rankers::pairGreater... Generating docs for compound Rankers::pairLess... Generating docs for namespace RDCatalog Generating docs for compound RDCatalog::Catalog... Generating docs for compound RDCatalog::CatalogEntry... Generating docs for compound RDCatalog::CatalogParams... Generating docs for compound RDCatalog::HierarchCatalog... Generating docs for nested compound RDCatalog::HierarchCatalog::vertex_entry_t... Generating docs for compound RDCatalog::LinearCatalog... Generating docs for namespace RDDataManip Generating docs for compound RDDataManip::MetricMatrixCalc... Generating docs for namespace RDDepict Generating docs for compound RDDepict::DepictException... Generating docs for compound RDDepict::EmbeddedAtom... Generating docs for compound RDDepict::EmbeddedFrag... Generating docs for compound RDDepict::gtIIPair... Generating docs for namespace RDFeatures Generating docs for compound RDFeatures::ExplicitFeature... Generating docs for compound RDFeatures::ImplicitFeature... Generating docs for namespace RDGeom Generating docs for compound RDGeom::Grid3D... Generating docs for compound RDGeom::GridException... Generating docs for compound RDGeom::Point... Generating docs for compound RDGeom::Point2D... Generating docs for compound RDGeom::Point3D... Generating docs for compound RDGeom::PointND... Generating docs for compound RDGeom::Transform2D... Generating docs for compound RDGeom::Transform3D... Generating docs for compound RDGeom::UniformGrid3D... Generating docs for namespace RDInfoTheory Generating docs for compound RDInfoTheory::BitCorrMatGenerator... Generating docs for compound RDInfoTheory::InfoBitRanker... Generating docs for namespace RDKit Generating docs for compound RDKit::AdditionalOutput... Generating docs for compound RDKit::AromaticAtomIterator_... Generating docs for compound RDKit::Atom... Generating docs for compound RDKit::AtomEnvironment... Generating docs for compound RDKit::AtomEnvironmentGenerator... Generating docs for compound RDKit::atomicData... Generating docs for compound RDKit::AtomInvariantsGenerator... Generating docs for compound RDKit::AtomIterator_... Generating docs for compound RDKit::AtomMonomerInfo... Generating docs for compound RDKit::AtomPDBResidueInfo... Generating docs for compound RDKit::AtomRingQuery... Generating docs for compound RDKit::BadFileException... Generating docs for compound RDKit::Bond... /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:207: 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/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Reaction.h:221: warning: The following parameters of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const are not documented: parameter 'numProducts' /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:415: 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 100 in file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:415: warning: The following parameters of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:100: 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/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:106: warning: The following parameters of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 are not documented: parameter 'matchVect' /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:176: warning: The following parameters 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=NULL, const std::map< int, DrawColour > *highlight_bond_map=NULL, const std::map< int, double > *highlight_radii=NULL, int confId=-1) are not documented: parameter 'highlight_bonds' /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:207: 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=NULL, const std::vector< std::vector< int > > *highlight_atoms=NULL, const std::vector< std::vector< int > > *highlight_bonds=NULL, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=NULL, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=NULL, const std::vector< std::map< int, double > > *highlight_radii=NULL, const std::vector< int > *confIds=NULL) /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:207: 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=NULL, const std::vector< std::vector< int > > *highlight_atoms=NULL, const std::vector< std::vector< int > > *highlight_bonds=NULL, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=NULL, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=NULL, const std::vector< std::map< int, double > > *highlight_radii=NULL, const std::vector< int > *confIds=NULL) /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:207: 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=NULL, const std::vector< std::vector< int > > *highlight_atoms=NULL, const std::vector< std::vector< int > > *highlight_bonds=NULL, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=NULL, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=NULL, const std::vector< std::map< int, double > > *highlight_radii=NULL, const std::vector< int > *confIds=NULL) /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/MolDraw2D.h:231: warning: The following parameters of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=NULL, const std::vector< std::vector< int > > *highlight_atoms=NULL, const std::vector< std::vector< int > > *highlight_bonds=NULL, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=NULL, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=NULL, const std::vector< std::map< int, double > > *highlight_radii=NULL, const std::vector< int > *confIds=NULL) are not documented: parameter 'highlight_bonds' parameter 'highlight_atom_maps' parameter 'highlight_bond_maps' parameter 'confIds' 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::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::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::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::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::FingerprintGenerator... Generating docs for compound RDKit::ForwardSDMolSupplier... Generating docs for compound RDKit::FPBReader... Generating docs for compound RDKit::FPHolderBase... Generating docs for compound RDKit::FragCatalogEntry... Generating docs for compound RDKit::FragCatGenerator... Generating docs for compound RDKit::FragCatParams... Generating docs for compound RDKit::FragFPGenerator... Generating docs for compound RDKit::GasteigerParams... Generating docs for compound RDKit::HasPropQuery... Generating docs for compound RDKit::HasPropWithValueQuery... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, std::string >... Generating docs for compound RDKit::HeteroatomIterator_... Generating docs for compound RDKit::larger_of... Generating docs for compound RDKit::ltDouble... Generating docs for compound RDKit::MatchingAtomIterator_... Generating docs for compound RDKit::MCSAtomCompareParameters... Generating docs for compound RDKit::MCSBondCompareParameters... Generating docs for compound RDKit::MCSParameters... Generating docs for compound RDKit::MCSProgressData... Generating docs for compound RDKit::MCSResult... Generating docs for compound RDKit::MolBundle... Generating docs for compound RDKit::MolCatalogEntry... Generating docs for compound RDKit::MolCatalogParams... Generating docs for compound RDKit::MolChemicalFeature... Generating docs for compound RDKit::MolChemicalFeatureDef... Generating docs for compound RDKit::MolChemicalFeatureFactory... Generating docs for compound RDKit::MolDraw2D... Generating docs for compound RDKit::MolDraw2DCairo... Generating docs for compound RDKit::MolDraw2DQt... Generating docs for compound RDKit::MolDraw2DSVG... Generating docs for compound RDKit::MolDraw2Dwx./build/rdkit-201809.1+dfsg/Code/GraphMol/Resonance.h:56: 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/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:322: 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 100 in file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:322: warning: The following parameters of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:206: warning: argument 'delimiter' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:206: warning: argument 'smilesColumn' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:206: warning: argument 'nameColumn' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:206: warning: argument 'titleLine' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers/MolSupplier.h:206: warning: argument 'sanitize' of command @param is not found in the argument list of RDKit::SmilesMolSupplier::SmilesMolSupplier(const std::string &fileName) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairGenerator.h:103: warning: The following parameters of RDKit::AtomPair::AtomPairAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const are not documented: parameter 'AdditionalOutput' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/AtomPairs.h:121: warning: The following parameters of RDKit::AtomPairs::getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< boost::uint32_t > *fromAtoms=0, const std::vector< boost::uint32_t > *ignoreAtoms=0, const std::vector< boost::uint32_t > *atomInvariants=0, bool includeChirality=false, bool use2D=true, int confId=-1) are not documented: parameter 'confId' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/FingerprintUtil.h:77: warning: The following parameters of RDKit::AtomPairs::getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false) are not documented: parameter 'includeChirality' /build/rdkit-201809.1+dfsg/Code/GraphMol/Canon.h:113: 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=0, const std::vector< std::string > *bondSymbols=0, bool doIsomericSmiles=false, bool doRandom=false) are not documented: parameter 'bondsInPlay' parameter 'bondSymbols' parameter 'doIsomericSmiles' parameter 'doRandom' /build/rdkit-201809.1+dfsg/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/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Lipinski.h:52: warning: The following parameters of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) are not documented: parameter 'useStrictDefinition' /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/USRDescriptor.h:79: warning: The following parameters of RDKit::Descriptors::USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int >> &atomIds, int confId=-1) are not documented: parameter 'atomIds' .. Generating docs for compound RDKit::MolDrawOptions... Generating docs for compound RDKit::MolHolder... Generating docs for compound RDKit::MolHolderBase... Generating docs for compound RDKit::MolPickler... Generating docs for compound RDKit::MolPicklerException... Generating docs for compound RDKit::MolSanitizeException... Generating docs for compound RDKit::MolSupplier... Generating docs for compound RDKit::MolWriter... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::MultiMolDraw2D... Generating docs for compound RDKit::PatternHolder... Generating docs for compound RDKit::PDBMolSupplier... Generating docs for compound RDKit::PDBWriter... Generating docs for compound RDKit::PeriodicTable... Generating docs for compound RDKit::QueryAtom... Generating docs for compound RDKit::QueryAtomIterator_... Generating docs for compound RDKit::QueryBond... Generating docs for compound RDKit::RandomSampleAllBBsStrategy... Generating docs for compound RDKit::RandomSampleStrategy... Generating docs for compound RDKit::RDAny... Generating docs for compound RDKit::RDProps... Generating docs for compound RDKit::RDValue... Generating docs for compound RDKit::ReactionFingerprintParams... Generating docs for compound RDKit::ReactionPickler... Generating docs for compound RDKit::ReactionPicklerException... Generating docs for compound RDKit::RecursiveStructureQuery... Generating docs for compound RDKit::ResonanceMolSupplier... Generating docs for compound RDKit::RGroupDecomposition... Generating docs for compound RDKit::RGroupDecompositionParameters... Generating docs for compound RDKit::RingInfo... Generating docs for compound RDKit::ROMol... Generating docs for compound RDKit::RWMol... Generating docs for compound RDKit::RxnSanitizeException... Generating docs for compound RDKit::SDMolSupplier... Generating docs for compound RDKit::SDWriter... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::SmilesMolSupplier... Generating docs for compound RDKit::SmilesParseException... Generating docs for compound RDKit::SmilesParserParams... Generating docs for compound RDKit::SmilesWriter... Generating docs for compound RDKit::Snapshot... Generating docs for compound RDKit::SparseIntVect... Generating docs for compound RDKit::StereoGroup... Generating docs for compound RDKit::SubstructLibrary... Generating docs for compound RDKit::TDTMolSupplier... Generating docs for compound RDKit::TDTWriter... Generating docs for compound RDKit::Trajectory... Generating docs for compound RDKit::UnimplementedFPException... Generating docs for namespace RDKit::AtomPair Generating docs for compound RDKit::AtomPair::AtomPairArguments... Generating docs for compound RDKit::AtomPair::AtomPairAtomEnv... Generating docs for compound RDKit::AtomPair::AtomPairAtomInvGenerator... Generating docs for compound RDKit::AtomPair::AtomPairEnvGenerator... Generating docs for namespace RDKit::AtomPairs Generating docs for namespace RDKit::Canon Generating docs for compound RDKit::Canon::AtomCompareFunctor... Generating docs for compound RDKit::Canon::bondholder... Generating docs for compound RDKit::Canon::canon_atom... Generating docs for compound RDKit::Canon::ChiralAtomCompareFunctor... Generating docs for compound RDKit::Canon::MolStackElem... Generating docs for compound RDKit::Canon::MolStackUnion... Generating docs for compound RDKit::Canon::SpecialChiralityAtomCompareFunctor... Generating docs for compound RDKit::Canon::SpecialSymmetryAtomCompareFunctor... Generating docs for namespace RDKit::common_properties Generating docs for namespace RDKit::constants 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::Properties... Generating docs for compound RDKit::Descriptors::PropertyFunctor... Generating docs for namespace RDKit::Descriptors::detail Generating d/build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:86: 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 100 in file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:86: warning: The following parameters of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:204: 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 100 in file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:204: warning: The following parameters of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:148: 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 100 in file /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/FilterMatchers.h:148: warning: The following parameters of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const are not documented: parameter 'matchVect' /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/MMPA.h:36: warning: The following parameters 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;!$(*=,#[!#6])]!@!=!#[*]") are not documented: parameter 'pattern' /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/MMPA.h:57: warning: The following parameters of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") are not documented: parameter 'pattern' /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.h:645: warning: The following parameters of RDKit::MolOps::getAdjacencyMatrix(const ROMol &mol, bool useBO=false, int emptyVal=0, bool force=false, const char *propNamePrefix=0, const boost::dynamic_bitset<> *bondsToUse=0) are not documented: parameter 'bondsToUse' /build/rdkit-201809.1+dfsg/Code/GraphMol/MolOps.h:257: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false) are not documented: parameter 'mergeUnmappedOnly' ocs for namespace RDKit::detail Generating docs for namespace RDKit::DGeomHelpers Generating docs for compound RDKit::DGeomHelpers::EmbedParameters... Generating docs for namespace RDKit::DTags Generating docs for namespace RDKit::EnumerationStrategyPickler Generating docs for namespace RDKit::EnumerationTypes Generating docs for namespace RDKit::FileParserUtils Generating docs for namespace RDKit::FilterMatchOps Generating docs for compound RDKit::FilterMatchOps::And... Generating docs for compound RDKit::FilterMatchOps::Not... Generating docs for compound RDKit::FilterMatchOps::Or... Generating docs for namespace RDKit::FMCS Generating docs for compound RDKit::FMCS::Composition2N... Generating docs for compound RDKit::FMCS::DuplicatedSeedCache... Generating docs for nested compound RDKit::FMCS::DuplicatedSeedCache::TKey... Generating docs for compound RDKit::FMCS::ExecStatistics... Generating docs for compound RDKit::FMCS::Graph... Generating docs for compound RDKit::FMCS::MaximumCommonSubgraph... Generating docs for compound RDKit::FMCS::MolFragment... Generating docs for compound RDKit::FMCS::NewBond... Generating docs for compound RDKit::FMCS::RingMatchTableSet... 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::Local Generating docs for namespace RDKit::MACCSFingerprints 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::Tools Generating docs for compound RDKit::MMFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::MMPA Generating docs for namespace RDKit::MolAlign Generating docs for compound RDKit::MolAlign::LAP... Generating docs for compound RDKit::MolAlign::MolAlignException... Generating docs for compound RDKit::MolAlign::MolHistogram... Generating docs for compound RDKit::MolAlign::O3A... Generating docs for compound RDKit::MolAlign::O3AConstraint... Generating docs for compound RDKit::MolAlign::O3AConstraintVect... Generating docs for compound RDKit::MolAlign::O3AFuncData... Generating docs for compound RDKit::MolAlign::SDM... Generating docs for namespace RDKit::MolDraw2D_detail Generating docs for namespace RDKit::MolDraw2DUtils Generating docs for namespace RDKit::MolFragmenter Generating docs for compound RDKit::MolFragmenter::FragmenterBondType... Generating docs for namespace RDKit::MolHash Generating docs for compound RDKit::MolHash::HashSet... Generating docs for namespace RDKit::MolInterchange Generating docs for compound RDKit::MolInterchange::JSONParseParameters... Generating docs for namespace RDKit::MolOps Generating docs for compound RDKit::MolOps::AdjustQueryParameters... Generating docs for namespace RDKit::MolShapes Generating docs for namespace RDKit::MolStandardize Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogEntry... Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogParams... Generating docs for compound RDKit::MolStandardize::AllowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::ChargeCorrection... Generating docs for compound RDKit::MolStandardize::CleanupParameters... Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::FragmentCatalogEntry... Generating docs for compound RDKit::MolStandardize::FragmentCatalogParams... Generating docs for compound RDKit::MolStandardize::FragmentRemover... Generating docs for compound RDKit::MolStandardize::FragmentValidation... Generating docs for compou/build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.h:189: warning: argument 'OutputType' of command @param is not found in the argument list of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=true, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.h:189: warning: argument 'radiu' of command @param is not found in the argument list of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=true, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.h:228: warning: The following parameters of RDKit::MorganFingerprint::getMorganGenerator(const unsigned int radius, const bool countSimulation=true, const bool includeChirality=false, const bool useBondTypes=true, const bool onlyNonzeroInvariants=false, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, BondInvariantsGenerator *bondInvariantsGenerator=nullptr, const std::uint32_t fpSize=2048, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const bool ownsAtomInvGen=false, const bool ownsBondInvGen=false) are not documented: parameter 'radius' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganGenerator.h:151: warning: The following parameters of RDKit::MorganFingerprint::MorganAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const are not documented: parameter 'AdditionalOutput' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/MorganFingerprints.h:152: warning: The following parameters of RDKit::MorganFingerprints::getHashedFingerprint(const ROMol &mol, unsigned int radius, unsigned int nBits=2048, std::vector< boost::uint32_t > *invariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=0) are not documented: parameter 'nBits' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:109: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::RDKitFP::getRDKitFPGenerator(const unsigned int minPath=1, const unsigned int maxPath=7, const bool useHs=true, const bool branchedPaths=true, const bool useBondOrder=true, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048, const bool ownsAtomInvGen=false) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:133: warning: The following parameters of RDKit::RDKitFP::getRDKitFPGenerator(const unsigned int minPath=1, const unsigned int maxPath=7, const bool useHs=true, const bool branchedPaths=true, const bool useBondOrder=true, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048, const bool ownsAtomInvGen=false) are not documented: parameter 'countSimulation' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:35: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::RDKitFP::RDKitFPArguments< OutputType >::RDKitFPArguments(unsigned int minPath, unsigned int maxPath, bool useHs, bool branchedPaths, bool useBondOrder, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:52: warning: The following parameters of RDKit::RDKitFP::RDKitFPArguments::RDKitFPArguments(unsigned int minPath, unsigned int maxPath, bool useHs, bool branchedPaths, bool useBondOrder, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) are not documented: parameter 'countSimulation' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:75: warning: The following parameters of RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const are not documented: parameter 'AdditionalOutput' /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:34: warning: The following parameters of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<> > *atomTypes=0) are not documented: parameter 'atomTypes' /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h:124: warning: argument 'operationThatFailed' of command @param is not found in the argument list of RDKit::RxnOps::sanitizeRxn(ChemicalReaction &rxn, unsigned int &operationsThatFailed, unsigned int sanitizeOps=SANITIZE_ALL, const MolOps::AdjustQueryParameters ¶ms=DefaultRxnAdjustParams()) /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/SanitizeRxn.h:155: warning: The following parameters of RDKit::RxnOps::sanitizeRxn(ChemicalReaction &rxn, unsigned int &operationsThatFailed, unsigned int sanitizeOps=SANITIZE_ALL, const MolOps::AdjustQueryParameters ¶ms=DefaultRxnAdjustParams()) are not documented: parameter 'operationsThatFailed' parameter 'params' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:87: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(const bool includeChirality=false, const uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048, const bool ownsAtomInvGen=false) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:108: warning: The following parameters of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(const bool includeChirality=false, const uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048, const bool ownsAtomInvGen=false) are not documented: parameter 'countSimulation' /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:33: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::TopologicalTorsionArguments< OutputType >::TopologicalTorsionArguments(const bool includeChirality, const uint32_t torsionAtomCount, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:44: warning: The following parameters of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality, const uint32_t torsionAtomCount, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) are not documented: parameter 'countSimulation' nd RDKit::MolStandardize::IsotopeValidation... Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser... Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKit::MolStandardize::MolVSValidation... Generating docs for compound RDKit::MolStandardize::MolVSValidations... Generating docs for compound RDKit::MolStandardize::NeutralValidation... Generating docs for compound RDKit::MolStandardize::NoAtomValidation... Generating docs for compound RDKit::MolStandardize::Normalizer... Generating docs for nested compound RDKit::MolStandardize::Normalizer::Product... Generating docs for compound RDKit::MolStandardize::RDKitValidation... Generating docs for compound RDKit::MolStandardize::Reionizer... Generating docs for compound RDKit::MolStandardize::TautomerCanonicalizer... 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::TautomerTransform... Generating docs for compound RDKit::MolStandardize::TransformCatalogEntry... Generating docs for compound RDKit::MolStandardize::TransformCatalogParams... Generating docs for compound RDKit::MolStandardize::Uncharger... Generating docs for compound RDKit::MolStandardize::ValidationErrorInfo... Generating docs for compound RDKit::MolStandardize::ValidationMethod... Generating docs for namespace RDKit::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::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::SLNParse Generating docs for compound RDKit::SLNParse::AttribType... Generating docs for namespace RDKit::SmartsWrite Generating docs for namespace RDKit::SmilesWrite Generating docs for namespace RDKit::StructureCheck Generating docs for compound RDKit::StructureCheck::AugmentedAtom... Generating docs for compound RDKit::StructureCheck::ChargeFix... Generating docs for compound RDKit::StructureCheck::IncEntry... Generating docs for compound RDKit::StructureCheck::Ligand... Generating docs for compound RDKit::StructureCheck::Neighbourhood... Generating docs for compound RDKit::StructureCheck::PathEntry... Generating docs for compound RDKit::StructureCheck::StructChecker... Generating docs for compound RDKit::StructureCheck::StructCheckerOptions... Generating docs for compound RDKit::StructureCheck::StructCheckTautomer... Generating docs for namespace RDKit::Subgraphs Generating docs for namespace RDKit::TopologicalTorsion Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionArguments... Generating docs for compound RDKit::Topologic/build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:57: warning: The following parameters of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false) const are not documented: parameter 'AdditionalOutput' /build/rdkit-201809.1+dfsg/Code/SimDivPickers/HierarchicalClusterPicker.h:80: warning: The following parameters of RDPickers::HierarchicalClusterPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize) const are not documented: parameter 'distMat' /build/rdkit-201809.1+dfsg/Code/SimDivPickers/MaxMinPicker.h:54: 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/rdkit-201809.1+dfsg/Code/SimDivPickers/MaxMinPicker.h:54: 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 alTorsion::TopologicalTorsionAtomEnv... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator... Generating docs for namespace RDKit::UFF Generating docs for namespace RDKit::UFF::Tools Generating docs for compound RDKit::UFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::Utils Generating docs for compound RDKit::Utils::LocaleSwitcher... Generating docs for namespace RDKit::Utils::detail Generating docs for namespace RDLog Generating docs for namespace RDNumeric Generating docs for compound RDNumeric::Matrix... Generating docs for compound RDNumeric::SquareMatrix... Generating docs for compound RDNumeric::SymmMatrix... Generating docs for compound RDNumeric::Vector... Generating docs for namespace RDNumeric::Alignments Generating docs for namespace RDNumeric::EigenSolvers Generating docs for namespace RDPickers Generating docs for compound RDPickers::DistPicker... Generating docs for compound RDPickers::HierarchicalClusterPicker... Generating docs for compound RDPickers::MaxMinPicker... Generating docs for compound RDPickers::MaxMinPickInfo... Generating docs for namespace RingUtils Generating docs for namespace SmilesParseOps Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... lookup cache used 15926/65536 hits=133999 misses=17233 finished... (cd /build/rdkit-201809.1+dfsg/Docs/Book; RDBASE=/build/rdkit-201809.1+dfsg /usr/bin/make html) make[2]: Entering directory '/build/rdkit-201809.1+dfsg/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/rdkit-201809.1+dfsg/Code/docs/* _build/html/cppapi sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v1.8.4 building [mo]: targets for 0 po files that are out of date building [html]: targets for 296 source files that are out of date updating environment: 296 added, 0 changed, 0 removed reading sources... [ 0%] BackwardsIncompatibleChanges reading sources... [ 0%] Cartridge reading sources... [ 1%] Cookbook reading sources... [ 1%] GettingStartedInPython reading sources... [ 1%] Install reading sources... [ 2%] Overview reading sources... [ 2%] RDKit_Book reading sources... [ 2%] api-docs reading sources... [ 3%] index reading sources... [ 3%] source/modules reading sources... [ 3%] source/rdkit reading sources... [ 4%] source/rdkit.Avalon reading sources... 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[100%] source/rdkit.utils.spiral /usr/lib/python3/dist-packages/recommonmark/parser.py:280: UserWarning: Unsupported inline type Hardbreak warn("Unsupported inline type " + inline.t) /build/rdkit-201809.1+dfsg/Docs/Book/GettingStartedInPython.rst:2720: WARNING: Block quote ends without a blank line; unexpected unindent. /build/rdkit-201809.1+dfsg/Docs/Book/GettingStartedInPython.rst:2729: WARNING: Unexpected indentation. WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.DSViewer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.aggCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.cairoCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.canvasbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.mplCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.qtCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.LazyGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.ScaffoldTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.testCombined' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst:2: WARNING: Title underline too short. rdkit.Chem.rdForceFieldHelpers module ================================= WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolDescriptors module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolInterchange module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst:2: WARNING: Title underline too short. rdkit.Chem.rdPartialCharges module ================================= WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst:2: WARNING: Title underline too short. rdkit.Chem.rdRGroupDecomposition module ================================= WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdStructChecker' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst:2: WARNING: Title underline too short. rdkit.Chem.rdSubstructLibrary module ================================= WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.HierarchyVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbReport' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.AnalyzeComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.BuildComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.murtagh_test' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.AdjustComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.BayesComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.CompositeRun' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildQuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildSigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Forest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.ID3' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.PruneTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.QuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.SigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Tree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.randomtest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.EnrichPlot' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.GrowComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.DistFunctions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNRegressionModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.PackageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.Packager' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.ClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.ActFuncs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.NetNode' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Network' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Trainers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ScreenComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.demo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'six' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw_qax' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.comhack' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' looking for now-outdated files... none found pickling environment... done checking consistency... /build/rdkit-201809.1+dfsg/Docs/Book/source/modules.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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WARNING: html_static_path entry '/build/rdkit-201809.1+dfsg/Docs/Book/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 297 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/build/rdkit-201809.1+dfsg/Docs/Book' (cd /build/rdkit-201809.1+dfsg/Docs/Book; RDBASE=/build/rdkit-201809.1+dfsg /usr/bin/make latexpdf) make[2]: Entering directory '/build/rdkit-201809.1+dfsg/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/rdkit-201809.1+dfsg/Code/docs/* _build/html/cppapi sphinx-build -b latex -d _build/doctrees . _build/latex Running Sphinx v1.8.4 making output directory... loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 296 added, 0 changed, 0 removed reading sources... 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WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.DSViewer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.aggCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.cairoCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.canvasbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.mplCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.qtCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.LazyGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.ScaffoldTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.testCombined' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst:2: WARNING: Title underline too short. rdkit.Chem.rdForceFieldHelpers module ================================= WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolDescriptors module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolInterchange module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst:2: WARNING: Title underline too short. rdkit.Chem.rdPartialCharges module ================================= WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst:2: WARNING: Title underline too short. rdkit.Chem.rdRGroupDecomposition module ================================= WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdStructChecker' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/rdkit-201809.1+dfsg/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst:2: WARNING: Title underline too short. rdkit.Chem.rdSubstructLibrary module ================================= WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.HierarchyVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbReport' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.AnalyzeComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.BuildComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.murtagh_test' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.AdjustComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.BayesComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.CompositeRun' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildQuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildSigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Forest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.ID3' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.PruneTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.QuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.SigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Tree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.randomtest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.EnrichPlot' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.GrowComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.DistFunctions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNRegressionModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.PackageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.Packager' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.ClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.ActFuncs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.NetNode' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Network' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Trainers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ScreenComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.demo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'six' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemdraw_qax' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.comhack' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' looking for now-outdated files... none found pickling environment... done checking consistency... /build/rdkit-201809.1+dfsg/Docs/Book/source/modules.rst: WARNING: document isn't included in any toctree done processing RDKit.tex...index Overview Install GettingStartedInPython RDKit_Book Cookbook Cartridge BackwardsIncompatibleChanges api-docs source/rdkit source/rdkit.Avalon source/rdkit.Avalon.pyAvalonTools source/rdkit.Chem source/rdkit.Chem.AtomPairs source/rdkit.Chem.AtomPairs.Pairs source/rdkit.Chem.AtomPairs.Sheridan source/rdkit.Chem.AtomPairs.Torsions source/rdkit.Chem.AtomPairs.Utils source/rdkit.Chem.ChemUtils source/rdkit.Chem.ChemUtils.AlignDepict source/rdkit.Chem.ChemUtils.BulkTester source/rdkit.Chem.ChemUtils.DescriptorUtilities source/rdkit.Chem.ChemUtils.SDFToCSV source/rdkit.Chem.ChemUtils.TemplateExpand source/rdkit.Chem.Draw source/rdkit.Chem.Draw.IPythonConsole source/rdkit.Chem.Draw.MolDrawing source/rdkit.Chem.Draw.SimilarityMaps source/rdkit.Chem.Draw.rdMolDraw2D source/rdkit.Chem.Draw.aggCanvas source/rdkit.Chem.Draw.cairoCanvas source/rdkit.Chem.Draw.canvasbase source/rdkit.Chem.Draw.mplCanvas source/rdkit.Chem.Draw.qtCanvas 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.LazyGenerator 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.ScaffoldTree 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.Subshape.testCombined 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.DSViewer 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.MCS 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.SATIS source/rdkit.Chem.SaltRemover source/rdkit.Chem.ShowMols 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.rdStructChecker source/rdkit.Chem.rdMolDescriptors source/rdkit.Chem.rdFingerprintGenerator source/rdkit.Chem.rdSLNParse source/rdkit.DataManip source/rdkit.DataManip.Metric source/rdkit.DataStructs source/rdkit.DataStructs.BitEnsemble source/rdkit.DataStructs.BitEnsembleDb source/rdkit.DataStructs.BitUtils source/rdkit.DataStructs.HierarchyVis source/rdkit.DataStructs.LazySignature source/rdkit.DataStructs.TopNContainer source/rdkit.DataStructs.VectCollection source/rdkit.Dbase source/rdkit.Dbase.DbConnection source/rdkit.Dbase.DbInfo source/rdkit.Dbase.DbModule source/rdkit.Dbase.DbReport source/rdkit.Dbase.DbResultSet source/rdkit.Dbase.DbUtils source/rdkit.Dbase.StorageUtils source/rdkit.DistanceGeometry source/rdkit.ForceField source/rdkit.Geometry 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.murtagh_test source/rdkit.ML.Composite source/rdkit.ML.Composite.AdjustComposite source/rdkit.ML.Composite.BayesComposite source/rdkit.ML.Composite.Composite 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.SplitData source/rdkit.ML.Data.Stats source/rdkit.ML.Data.Transforms source/rdkit.ML.DecTree source/rdkit.ML.DecTree.BuildQuantTree source/rdkit.ML.DecTree.BuildSigTree source/rdkit.ML.DecTree.CrossValidate source/rdkit.ML.DecTree.DecTree source/rdkit.ML.DecTree.Forest source/rdkit.ML.DecTree.ID3 source/rdkit.ML.DecTree.PruneTree source/rdkit.ML.DecTree.QuantTree source/rdkit.ML.DecTree.SigTree source/rdkit.ML.DecTree.Tree source/rdkit.ML.DecTree.TreeUtils source/rdkit.ML.DecTree.TreeVis source/rdkit.ML.DecTree.randomtest 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.KNN source/rdkit.ML.KNN.CrossValidate source/rdkit.ML.KNN.DistFunctions source/rdkit.ML.KNN.KNNClassificationModel source/rdkit.ML.KNN.KNNModel source/rdkit.ML.KNN.KNNRegressionModel source/rdkit.ML.MLUtils source/rdkit.ML.MLUtils.VoteImg source/rdkit.ML.ModelPackage source/rdkit.ML.ModelPackage.PackageUtils source/rdkit.ML.ModelPackage.Packager source/rdkit.ML.NaiveBayes source/rdkit.ML.NaiveBayes.ClassificationModel source/rdkit.ML.NaiveBayes.CrossValidate source/rdkit.ML.Neural source/rdkit.ML.Neural.ActFuncs source/rdkit.ML.Neural.CrossValidate source/rdkit.ML.Neural.NetNode source/rdkit.ML.Neural.Network source/rdkit.ML.Neural.Trainers source/rdkit.ML.SLT source/rdkit.ML.SLT.Risk source/rdkit.ML.Scoring source/rdkit.ML.Scoring.Scoring source/rdkit.ML.AnalyzeComposite source/rdkit.ML.BuildComposite source/rdkit.ML.CompositeRun source/rdkit.ML.EnrichPlot source/rdkit.ML.GrowComposite source/rdkit.ML.MatOps source/rdkit.ML.ScreenComposite source/rdkit.ML.files source/rdkit.Numerics source/rdkit.SimDivFilters source/rdkit.SimDivFilters.SimilarityPickers 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.NodeLib.demo 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.chemdraw source/rdkit.utils.chemdraw_qax source/rdkit.utils.chemutils source/rdkit.utils.comhack source/rdkit.utils.fileutils source/rdkit.utils.listutils source/rdkit.utils.spiral source/rdkit.RDConfig source/rdkit.RDLogger source/rdkit.RDPaths source/rdkit.RDRandom source/rdkit.TestRunner source/rdkit.six resolving references... writing... done copying images... 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 108--109 []\T1/ptm/m/n/10 Cheminformatics nodes for KN-IME (dis-tributed from the KN-IME com-mu-nity site: [1] LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 202. [2] [3] [4] Chapter 2. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [5] [6] [7] [8] [9] Underfull \hbox (badness 10000) in paragraph at lines 709--710 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [10] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [11] Underfull \hbox (badness 10000) in paragraph at lines 807--808 []\T1/ptm/m/n/10 Add \T1/pcr/m/n/10 #define BOOST_PYTHON_NO_PY_SIGNATURES \T1/p tm/m/n/10 at the top of \T1/pcr/m/n/10 Code/GraphMol/Wrap/ [12] [13] Underfull \hbox (badness 10000) in paragraph at lines 988--990 []\T1/ptm/m/n/10 Run cmake. Here's an ex-am-ple ba-sic com-mand line for 64bit win-dows that will down- Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 load the InChI and Avalon toolkit sources from the InChI Trust a nd Source-Forge repos- Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 i-to-ries, re-spec-tively, and build the Post-greSQL car-tridge for the in-stalled ver-sion of Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 Post-greSQL: \T1/pcr/m/n/10 cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/ Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" [14] Underfull \hbox (badness 10000) in paragraph at lines 998--999 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" Underfull \hbox (badness 10000) in paragraph at lines 1004--1005 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [15] [16] Chapter 3. 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[69 <./picture_9.png (PNG copy)>] [70 <./picture_8.png> <./picture_7.png (PNG c opy)>] [71 <./picture_10.png> <./picture_12.png>] [72 <./picture_11.png>] [73] Overfull \hbox (53.45044pt too wide) in paragraph at lines 4709--4709 [] Underfull \hbox (badness 10000) in paragraph at lines 4709--4709 [74] [75] [76] [77] [78] [79] LaTeX Warning: Hyper reference `RDKit_Book:ph4-figure' on page 80 undefined on input line 5165. 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[87] [88 <./indole1.png>] Overfull \vbox (2.48352pt too high) detected at line 5882 [89] [90] [91] Overfull \vbox (1.52577pt too high) detected at line 6067 [92] [93] [94] Overfull \vbox (2.13905pt too high) detected at line 6246 [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 6279--6280 []\T1/ptm/m/n/10 IPython note-book: [][]$http : / / nbviewer . ipython . org / gist / greglandrum / 8351725$[][] [][]$https : / / gist . github . com / gregla ndrum / [97 <./similarity_map_rf.png>] [98] [99] Underfull \vbox (badness 10000) detected at line 6505 Overfull \vbox (2.68169pt too high) detected at line 6505 [100] [101] [102] Chapter 6. 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[113] [114] [115] [116] [117] [118] [119] [120] Chapter 7. [121] [122] Chapter 8. [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] Chapter 9. [141] [142] Chapter 10. No file RDKit.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. [143] (./RDKit.aux) Package rerunfilecheck Warning: File `RDKit.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on RDKit.pdf (147 pages, 1593103 bytes). Transcript written on RDKit.log. Latexmk: Index file 'RDKit.idx' was written Latexmk: Missing input file: 'RDKit.ind' from line 'No file RDKit.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'RDKit.pdf' Rule 'makeindex RDKit.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'RDKit.idx' Non-existent destination files: 'RDKit.ind' ------------ Run number 1 of rule 'makeindex RDKit.idx' ------------ ------------ Running 'makeindex -s python.ist -o "RDKit.ind" "RDKit.idx"' ------------ === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex RDKit.idx'... This is makeindex, version 2.15 [TeX Live 2019/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file RDKit.idx...done (0 entries accepted, 0 rejected). Nothing written in RDKit.ind. Transcript written in RDKit.ilg. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 108--109 []\T1/ptm/m/n/10 Cheminformatics nodes for KN-IME (dis-tributed from the KN-IME com-mu-nity site: [1] LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 202. [2] [3] [4] Chapter 2. [5] [6] [7] [8] [9] Underfull \hbox (badness 10000) in paragraph at lines 709--710 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [10] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [11] Underfull \hbox (badness 10000) in paragraph at lines 807--808 []\T1/ptm/m/n/10 Add \T1/pcr/m/n/10 #define BOOST_PYTHON_NO_PY_SIGNATURES \T1/p tm/m/n/10 at the top of \T1/pcr/m/n/10 Code/GraphMol/Wrap/ [12] [13] Underfull \hbox (badness 10000) in paragraph at lines 988--990 []\T1/ptm/m/n/10 Run cmake. Here's an ex-am-ple ba-sic com-mand line for 64bit win-dows that will down- Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 load the InChI and Avalon toolkit sources from the InChI Trust a nd Source-Forge repos- Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 i-to-ries, re-spec-tively, and build the Post-greSQL car-tridge for the in-stalled ver-sion of Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 Post-greSQL: \T1/pcr/m/n/10 cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/ Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" [14] Underfull \hbox (badness 10000) in paragraph at lines 998--999 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" Underfull \hbox (badness 10000) in paragraph at lines 1004--1005 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [15] [16] Chapter 3. [17] Underfull \hbox (badness 10000) in paragraph at lines 1094--1095 []\T1/ptm/m/n/10 displays a mes-sage like: \T1/pcr/m/n/10 [12:18:01] Explicit v alence for atom # 1 O greater than [18] [19] [20] [21] [22] [23] [24] Underfull \hbox (badness 10000) in paragraph at lines 1621--1623 []\T1/ptm/m/n/10 Another op-tion for Com-pute2DCoords al-lows you to gen-er-ate 2D de-pic-tions for molecules that Underfull \hbox (badness 7649) in paragraph at lines 1621--1623 \T1/ptm/m/n/10 closely mimic 3D con-for-ma-tions. This is avail-able us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem.AllChem. [25 <./picture_1.png (PNG copy)> <./picture_0.png (PNG copy)> <./picture_3.png (PNG copy)>] Underfull \hbox (badness 10000) in paragraph at lines 1641--1646 []\T1/ptm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/pcr/m/n/10 rdkit.Chem.rdDepictor. [26 <./picture_2.png> <./picture_4.png>] [27] [28] [29 <./cdk2_mol1.png> <./cdk 2_mol2.png>] [30 <./cdk2_molgrid.png>] [31 <./cdk2_molgrid_aligned.png (PNG cop y)>] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42 <./mfp2_bit872.png> <./rdk_bit1553.png> <./rdk_bit1553_2.png>] [43] Overfull \vbox (9.6296pt too high) detected at line 2819 [44 <./similarity_map_fp1.png>] [45 <./similarity_map_fp2.png>] [46 <./similari ty_map_fp3.png>] [47] [48 <./similarity_map_charges.png>] [49 <./similarity_map _crippen.png>] [50] [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 6792) in paragraph at lines 3562--3565 []\T1/ptm/m/n/10 Or we can use the bit rank-ing func-tion-al-ity from the \T1/p cr/m/n/10 rdkit.ML.InfoTheory.rdInfoTheory. [59] [60] [61 <./picture_6.png>] [62] Underfull \hbox (badness 10000) in paragraph at lines 3882--3886 []|\T1/ptm/m/n/10 Wildman and Crip-pen \T1/ptm/m/it/10 JCICS Underfull \hbox (badness 10000) in paragraph at lines 3892--3896 []|\T1/ptm/m/n/10 Wildman and Crip-pen \T1/ptm/m/it/10 JCICS Overfull \hbox (26.64615pt too wide) in paragraph at lines 3960--3961 []|\T1/ptm/m/n/10 Num{Aromatic,Saturated,Aliphatic}Rings| Overfull \hbox (91.89552pt too wide) in paragraph at lines 3965--3966 []|\T1/ptm/m/n/10 Num{Aromatic,Saturated,Aliphatic}{Hetero,Carbo}cycles| Underfull \hbox (badness 10000) in paragraph at lines 3994--3997 []|\T1/ptm/m/n/10 Number of bridge-head atoms Overfull \hbox (150.19545pt too wide) in paragraph at lines 4008--4010 [] Underfull \hbox (badness 10000) in paragraph at lines 4008--4010 \T1/ptm/m/n/10 to the orig-i-nal Underfull \hbox (badness 10000) in paragraph at lines 4027--4030 \T1/ptm/m/n/10 tions [][]$http : / / www . chemcomp . com / Underfull \hbox (badness 10000) in paragraph at lines 4036--4040 \T1/ptm/m/n/10 tri-bu-tions [][]$http : / / www . chemcomp . Underfull \hbox (badness 10000) in paragraph at lines 4046--4050 \T1/ptm/m/n/10 tri-bu-tions [][]$http : / / www . chemcomp . 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[69 <./picture_9.png (PNG copy)>] [70 <./picture_8.png> <./picture_7.png (PNG c opy)>] [71 <./picture_10.png> <./picture_12.png>] [72 <./picture_11.png>] [73] Overfull \hbox (53.45044pt too wide) in paragraph at lines 4709--4709 [] Underfull \hbox (badness 10000) in paragraph at lines 4709--4709 [74] [75] [76] [77] [78] [79] [80] [81 <./picture_10.jpg>] Overfull \vbox (2.72571pt too high) detected at line 5369 [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 mol-Rxn-Com-po- [84] [85] [86] Chapter 5. [87] [88 <./indole1.png>] Overfull \vbox (2.48352pt too high) detected at line 5882 [89] [90] [91] Overfull \vbox (1.52577pt too high) detected at line 6067 [92] [93] [94] Overfull \vbox (2.13905pt too high) detected at line 6246 [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 6279--6280 []\T1/ptm/m/n/10 IPython note-book: [][]$http : / / nbviewer . ipython . org / gist / greglandrum / 8351725$[][] [][]$https : / / gist . github . com / gregla ndrum / [97 <./similarity_map_rf.png>] [98] [99] Underfull \vbox (badness 10000) detected at line 6505 Overfull \vbox (2.68169pt too high) detected at line 6505 [100] [101] [102] Chapter 6. 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[113] [114] [115] [116] [117] [118] [119] [120] Chapter 7. [121] [122] Chapter 8. [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] Chapter 9. [141] [142] Chapter 10. (./RDKit.ind) [143] (./RDKit.aux) LaTeX Warning: There were undefined references. LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on RDKit.pdf (151 pages, 1623130 bytes). Transcript written on RDKit.log. 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LaTeX Warning: Label `BackwardsIncompatibleChanges:license' multiply defined. ) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./RDKit.out) (./RDKit.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./RDKit.toc [1] [2] [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [4]) [5] [6] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Underfull \hbox (badness 10000) in paragraph at lines 108--109 []\T1/ptm/m/n/10 Cheminformatics nodes for KN-IME (dis-tributed from the KN-IME com-mu-nity site: [1] LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 202. [2] [3] [4] Chapter 2. [5] [6] [7] [8] [9] Underfull \hbox (badness 10000) in paragraph at lines 709--710 []\T1/ptm/m/n/10 You can en-able sup-port for the Avalon toolkit by adding the ar-gu-ment [10] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [11] Underfull \hbox (badness 10000) in paragraph at lines 807--808 []\T1/ptm/m/n/10 Add \T1/pcr/m/n/10 #define BOOST_PYTHON_NO_PY_SIGNATURES \T1/p tm/m/n/10 at the top of \T1/pcr/m/n/10 Code/GraphMol/Wrap/ [12] [13] Underfull \hbox (badness 10000) in paragraph at lines 988--990 []\T1/ptm/m/n/10 Run cmake. Here's an ex-am-ple ba-sic com-mand line for 64bit win-dows that will down- Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 load the InChI and Avalon toolkit sources from the InChI Trust a nd Source-Forge repos- Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 i-to-ries, re-spec-tively, and build the Post-greSQL car-tridge for the in-stalled ver-sion of Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/ptm/m/n/10 Post-greSQL: \T1/pcr/m/n/10 cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/ Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/pcr/m/n/10 boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 988--990 \T1/pcr/m/n/10 -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\Postgre SQL\9.5" [14] Underfull \hbox (badness 10000) in paragraph at lines 998--999 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" Underfull \hbox (badness 10000) in paragraph at lines 1004--1005 []\T1/pcr/m/n/10 "C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresq l-9.5" [15] [16] Chapter 3. [17] Underfull \hbox (badness 10000) in paragraph at lines 1094--1095 []\T1/ptm/m/n/10 displays a mes-sage like: \T1/pcr/m/n/10 [12:18:01] Explicit v alence for atom # 1 O greater than [18] [19] [20] [21] [22] [23] [24] Underfull \hbox (badness 10000) in paragraph at lines 1621--1623 []\T1/ptm/m/n/10 Another op-tion for Com-pute2DCoords al-lows you to gen-er-ate 2D de-pic-tions for molecules that Underfull \hbox (badness 7649) in paragraph at lines 1621--1623 \T1/ptm/m/n/10 closely mimic 3D con-for-ma-tions. This is avail-able us-ing the func-tion \T1/pcr/m/n/10 rdkit.Chem.AllChem. [25 <./picture_1.png (PNG copy)> <./picture_0.png (PNG copy)> <./picture_3.png (PNG copy)>] Underfull \hbox (badness 10000) in paragraph at lines 1641--1646 []\T1/ptm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/pcr/m/n/10 rdkit.Chem.rdDepictor. [26 <./picture_2.png> <./picture_4.png>] [27] [28] [29 <./cdk2_mol1.png> <./cdk 2_mol2.png>] [30 <./cdk2_molgrid.png>] [31 <./cdk2_molgrid_aligned.png (PNG cop y)>] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42 <./mfp2_bit872.png> <./rdk_bit1553.png> <./rdk_bit1553_2.png>] [43] Overfull \vbox (9.6296pt too high) detected at line 2819 [44 <./similarity_map_fp1.png>] [45 <./similarity_map_fp2.png>] [46 <./similari ty_map_fp3.png>] [47] [48 <./similarity_map_charges.png>] [49 <./similarity_map _crippen.png>] [50] [51] [52] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 6792) in paragraph at lines 3562--3565 []\T1/ptm/m/n/10 Or we can use the bit rank-ing func-tion-al-ity from the \T1/p cr/m/n/10 rdkit.ML.InfoTheory.rdInfoTheory. [59] [60] [61 <./picture_6.png>] [62] Underfull \hbox (badness 10000) in paragraph at lines 3882--3886 []|\T1/ptm/m/n/10 Wildman and Crip-pen \T1/ptm/m/it/10 JCICS Underfull \hbox (badness 10000) in paragraph at lines 3892--3896 []|\T1/ptm/m/n/10 Wildman and Crip-pen \T1/ptm/m/it/10 JCICS Overfull \hbox (26.64615pt too wide) in paragraph at lines 3960--3961 []|\T1/ptm/m/n/10 Num{Aromatic,Saturated,Aliphatic}Rings| Overfull \hbox (91.89552pt too wide) in paragraph at lines 3965--3966 []|\T1/ptm/m/n/10 Num{Aromatic,Saturated,Aliphatic}{Hetero,Carbo}cycles| Underfull \hbox (badness 10000) in paragraph at lines 3994--3997 []|\T1/ptm/m/n/10 Number of bridge-head atoms Overfull \hbox (150.19545pt too wide) in paragraph at lines 4008--4010 [] Underfull \hbox (badness 10000) in paragraph at lines 4008--4010 \T1/ptm/m/n/10 to the orig-i-nal Underfull \hbox (badness 10000) in paragraph at lines 4027--4030 \T1/ptm/m/n/10 tions [][]$http : / / www . chemcomp . com / Underfull \hbox (badness 10000) in paragraph at lines 4036--4040 \T1/ptm/m/n/10 tri-bu-tions [][]$http : / / www . chemcomp . 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[69 <./picture_9.png (PNG copy)>] [70 <./picture_8.png> <./picture_7.png (PNG c opy)>] [71 <./picture_10.png> <./picture_12.png>] [72 <./picture_11.png>] [73] Overfull \hbox (53.45044pt too wide) in paragraph at lines 4709--4709 [] Underfull \hbox (badness 10000) in paragraph at lines 4709--4709 [74] [75] [76] [77] [78] [79] [80] [81 <./picture_10.jpg>] Overfull \vbox (2.72571pt too high) detected at line 5369 [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 5601--5601 []\T1/ptm/m/n/10 mol-Rxn-Com-po- [84] [85] [86] Chapter 5. [87] [88 <./indole1.png>] Overfull \vbox (2.48352pt too high) detected at line 5882 [89] [90] [91] Overfull \vbox (1.52577pt too high) detected at line 6067 [92] [93] [94] Overfull \vbox (2.13905pt too high) detected at line 6246 [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 6279--6280 []\T1/ptm/m/n/10 IPython note-book: [][]$http : / / nbviewer . ipython . org / gist / greglandrum / 8351725$[][] [][]$https : / / gist . github . com / gregla ndrum / [97 <./similarity_map_rf.png>] [98] [99] Underfull \vbox (badness 10000) detected at line 6505 Overfull \vbox (2.68169pt too high) detected at line 6505 [100] [101] [102] Chapter 6. [103] [104] [105] Overfull \hbox (232.24419pt too wide) in paragraph at lines 6740--6740 []\T1/pcr/m/n/9 CC(C)C[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N2c3cc ccc3[C[]@[][]@[]](O)(C[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]3[]NC([]=[]O) c4ccccc4N4C([]=[]O)c5ccccc5NC34)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]N1C([ ]=[]O)C(CCCNC([]=[]O)OCc1ccccc1)NC([]=[]O)OC(C)(C)C| Overfull \hbox (86.44435pt too wide) in paragraph at lines 6741--6741 []\T1/pcr/m/n/9 CC(C)C[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N2c3cc ccc3[C[]@[][]@[]](O)(C[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]3[]NC([]=[]O) c4ccccc4N4C([]=[]O)c5ccccc5NC34)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]N1C([ ]=[]O)CCC([]=[]O)[O[]- Underfull \vbox (badness 1383) detected at line 6747 [106] Overfull \hbox (372.64403pt too wide) in paragraph at lines 6789--6789 []\T1/pcr/m/n/9 CNCC([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCN[]= []C(N)N)C([]=[]O)N1C[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]C[C[]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]( Cc1ccc(O)cc1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C([]=[]O)N[C[]@[][ ]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1c[nH]cn1)C([]=[]O)N1CCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc 1ccccc1)C([]=[]O| Overfull \hbox (372.64403pt too wide) in paragraph at lines 6791--6791 []\T1/pcr/m/n/9 CNCCCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC([]=[]O)[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CCCCNC)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(O)cc 1)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)NC([]=[]O)[C[]@[][]\T1/pcr /b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc1ccccc1)NC([]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C| Overfull \hbox (372.64403pt too wide) in paragraph at lines 6793--6793 []\T1/pcr/m/n/9 CC([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc2ccccc2c 1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CO)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(O)c c1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCCNC(C)C)C([]=[]O)N[C[]@[] []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1| Overfull \hbox (372.64403pt too wide) in paragraph at lines 6795--6795 []\T1/pcr/m/n/9 CC([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc2ccccc2c 1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CO)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(O)c c1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCN[]=[]C(N)N)C([]=[]O)N[C[ ]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1| Overfull \hbox (372.64403pt too wide) in paragraph at lines 6797--6797 []\T1/pcr/m/n/9 CC([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc2ccccc2c 1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CO)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(O)c c1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCN[]=[]C(N)N)C([]=[]O)N[C[ ]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1| Overfull \hbox (372.64403pt too wide) in paragraph at lines 6799--6799 []\T1/pcr/m/n/9 CC([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc2ccccc2c 1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]\T1/p cr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1 /pcr/m/n/9 ](CO)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc1ccc(O)c c1)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCCNC1CCCCC1)C([]=[]O)N[C[] @[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](| Overfull \hbox (351.04405pt too wide) in paragraph at lines 6802--6802 [][]\T1/pcr/m/n/9 N)NS([]=[]O)([]=[]O)c1c(C)c(C)c2c(c1C)CCC(C)(C)O2)C([]=[]O)N[ C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C([]=[]O)NCC([]=[]O)N[C[]@[][]\T1/pcr/b/n/ 9 @H[]\T1/pcr/m/n/9 ](COC(C)(C)C)C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m /n/9 ](CCCCNC([]=[]O)c1ccccc1N)C([]=[]O)NCC([]=[]O)O)[C[]@[][]\T1/pcr/b/n/9 @H[ ]\T1/pcr/m/n/9 ](C)OC(C)(C)C| Overfull \hbox (372.64403pt too wide) in paragraph at lines 6803--6803 []\T1/pcr/m/n/9 CC(C)C[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]c3ccccc23)NC([]=[ ]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[] \T1/pcr/m/n/9 ](NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCCN)NC([]=[]O )[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCC(N)[]=[]O)NC| Overfull \hbox (426.64397pt too wide) in paragraph at lines 6804--6804 []|\T1/pcr/m/n/9 ([]=[]O)CNC([]=[]O)CN)CSSC[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m /n/9 ](C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccc(O)cc2)C([]=[ ]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)C([]=[]O)N[C[]\T1/pcr/b/n/9 @ H[]\T1/pcr/m/n/9 ](C([]=[]O)NCC([]=[]O)NCC(N)[]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[] \T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]cn2 )NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[]O)CNC| Overfull \hbox (372.64403pt too wide) in paragraph at lines 6808--6808 []\T1/pcr/m/n/9 CC1(C)SSC(C)(C)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C([]= []O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]cn2)C([]=[]O)N2CCC[C[]\ T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)C([]=[]O)O)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ] (Cc2ccc(O)cc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[ 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](CCCCNC([]=[]O)c1ccccc1N)C([]=[]O)NCC([]=[]O)O)[C[]@[][]\T1/pcr/b/n/9 @H[ ]\T1/pcr/m/n/9 ](C)OC(C)(C)C| Overfull \hbox (388.84401pt too wide) in paragraph at lines 6830--6830 []\T1/pcr/m/n/9 CC(C)C[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O) [C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]([C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C)O)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]c3ccccc23)NC([]=[ ]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C(C)C)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[] \T1/pcr/m/n/9 ](NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCCN)NC([]=[]O )[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]CCCN2C([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCC(N)[]=[]O)NC([]=[]O| Overfull \hbox (442.84395pt too wide) in paragraph at lines 6831--6831 []|\T1/pcr/m/n/9 )CNC([]=[]O)CN)CSSC[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ]( C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccc(O)cc2)C([]=[]O)N[C[ ]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CO)C([]=[]O)N[C[]\T1/pcr/b/n/9 @H[]\T1/ pcr/m/n/9 ](C([]=[]O)NCC([]=[]O)NCC(N)[]=[]O)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr /m/n/9 ](C)O)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]cn2)NC([]= []O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2ccccc2)NC([]=[]O)CNC([]=[]O)[C| Overfull \hbox (388.84401pt too wide) in paragraph at lines 6833--6833 []\T1/pcr/m/n/9 NC(N)[]=[]NCCC[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](NC([]=[]O)[ C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](N)CC([]=[]O)O)C([]=[]O)N[C[]\T1/pcr/b /n/9 @H[]\T1/pcr/m/n/9 ][]1[]CCSSC[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C( []=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]cn2)C([]=[]O)N2CCC[C []\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T 1/pcr/m/n/9 ](Cc2ccccc2)C([]=[]O)O)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/ 9 ](Cc2ccc(O)cc| Overfull \hbox (388.84401pt too wide) in paragraph at lines 6835--6835 []\T1/pcr/m/n/9 CC1(C)SSC(C)(C)[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](C([]= []O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](Cc2c[nH]cn2)C([]=[]O)N2CCC[C[]\ T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]2[]C([]=[]O)N[C[]@[][]\T1/pcr/b/n/9 @H[]\T1/p cr/m/n/9 ](Cc2ccccc2)C([]=[]O)O)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ] (Cc2ccc(O)cc2)NC([]=[]O)[C[]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ][]1[]NC([]=[]O)[C[ ]\T1/pcr/b/n/9 @H[]\T1/pcr/m/n/9 ](CCCN[]=[]C(N)N)NC([]=[]| Overfull \vbox (13.68167pt too high) detected at line 6845 [108] Overfull \hbox (21.64442pt too wide) in paragraph at lines 6858--6858 []\T1/pcr/m/n/9 Cn1c(Nc2c(Cl)ccc(CNC([]=[]O)C(C)(C)C)c2Cl)nc2cc(C([]=[]O)Nc3ccc c(C(F)(F)F)n3)c(N3CCC(F)(F)C3)cc21| Overfull \hbox (21.64442pt too wide) in paragraph at lines 6894--6894 []\T1/pcr/m/n/9 Cn1c(Nc2c(Cl)ccc(CNC([]=[]O)C(C)(C)C)c2Cl)nc2cc(C([]=[]O)Nc3ccc c(C(F)(F)F)n3)c(N3CCC(F)(F)C3)cc21| [109] Overfull \hbox (21.64442pt too wide) in paragraph at lines 6917--6917 []\T1/pcr/m/n/9 Cn1c(Nc2c(Cl)ccc(CNC([]=[]O)C(C)(C)C)c2Cl)nc2cc(C([]=[]O)Nc3ccc c(C(F)(F)F)n3)c(N3CCC(F)(F)C3)cc21| [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] Chapter 7. [121] [122] Chapter 8. [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] Chapter 9. [141] [142] Chapter 10. (./RDKit.ind) [143] (./RDKit.aux) LaTeX Warning: There were undefined references. LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on RDKit.pdf (151 pages, 1623130 bytes). Transcript written on RDKit.log. Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Latexmk: List of undefined refs and citations: Label `BackwardsIncompatibleChanges:backwards-incompatible-changes' multiply defined Label `BackwardsIncompatibleChanges:changes-to-ringmatchesringonly-option-in-the-mcs-code' multiply defined Label `BackwardsIncompatibleChanges:getatomsmiles-generates-isomeric-smiles-by-default' multiply defined Label `BackwardsIncompatibleChanges:license' multiply defined Label `BackwardsIncompatibleChanges:moltomolblock-generates-a-2d-conformation-when-the-includestereo-flag-is-set' multiply defined Label `BackwardsIncompatibleChanges:moltosmiles-generates-isomeric-smiles-by-default' multiply defined Label `BackwardsIncompatibleChanges:release-2018-03' multiply defined Label `BackwardsIncompatibleChanges:release-2018-09' multiply defined Label `BackwardsIncompatibleChanges:the-conformation-generation-code-now-uses-etkdg-by-default' multiply defined Label `BackwardsIncompatibleChanges:the-conformation-generation-code-now-uses-etkdg-by-default-when-called-from-python' multiply defined Label `Cartridge:adjusting-the-similarity-cutoff' multiply defined Label `Cartridge:configuration' multiply defined Label `Cartridge:connectivity-descriptors' multiply defined Label `Cartridge:creating-a-database-from-a-file' multiply defined Label `Cartridge:creating-databases' multiply defined Label `Cartridge:descriptors' multiply defined Label `Cartridge:fingerprint-i-o' multiply defined Label `Cartridge:fingerprint-related' multiply defined Label `Cartridge:functions' multiply defined Label `Cartridge:generating-fingerprints' multiply defined Label `Cartridge:introduction' multiply defined Label `Cartridge:license' multiply defined Label `Cartridge:loading-chembl' multiply defined Label `Cartridge:mcs' multiply defined Label `Cartridge:molecule-comparison' multiply defined Label `Cartridge:molecule-i-o-and-validation' multiply defined Label `Cartridge:molecule-related' multiply defined Label `Cartridge:new-types' multiply defined Label `Cartridge:operators' multiply defined Label `Cartridge:other' multiply defined Label `Cartridge:parameters' multiply defined Label `Cartridge:reference-guide' multiply defined Label `Cartridge:similarity-search' multiply defined Label `Cartridge:similarity-searches' multiply defined Label `Cartridge:smarts-based-queries' multiply defined Label `Cartridge:substructure-and-exact-structure-search' multiply defined Label `Cartridge:substructure-operations' multiply defined Label `Cartridge:substructure-searches' multiply defined Label `Cartridge:the-rdkit-database-cartridge' multiply defined Label `Cartridge:tuning-queries' multiply defined Label `Cartridge:tutorial' multiply defined Label `Cartridge:using-stereochemistry' multiply defined Label `Cartridge:using-the-cartridge-from-python' multiply defined Label `Cartridge:using-the-mcs-code' multiply defined Label `Cartridge:what-is-this' multiply defined Label `Cartridge:working-with-fingerprints' multiply defined Label `Cookbook:cleaning-up-heterocycles' multiply defined Label `Cookbook:clustering-molecules' multiply defined Label `Cookbook:d-functionality-in-the-rdkit' multiply defined Label `Cookbook:details' multiply defined Label `Cookbook:introduction' multiply defined Label `Cookbook:license' multiply defined Label `Cookbook:manipulating-molecules' multiply defined Label `Cookbook:miscellaneous-topics' multiply defined Label `Cookbook:neutralizing-charged-molecules' multiply defined Label `Cookbook:parallel-conformation-generation' multiply defined Label `Cookbook:rdkit-cookbook' multiply defined Label `Cookbook:rmsd-calculation-between-n-molecules' multiply defined Label `Cookbook:using-a-different-aromaticity-model' multiply defined Label `Cookbook:using-custom-mcs-atom-types' multiply defined Label `Cookbook:using-scikit-learn-with-rdkit' multiply defined Label `Cookbook:what-is-this' multiply defined Label `Install:advanced' multiply defined Label `Install:building-from-source' multiply defined Label `Install:building-from-the-command-line-recommended' multiply defined Label `Install:building-the-java-wrappers' multiply defined Label `Install:building-the-rdkit' multiply defined Label `Install:conda-forge-package' multiply defined Label `Install:cross-platform-under-anaconda-python-fastest-install' multiply defined Label `Install:disabling-the-python-wrappers' multiply defined Label `Install:extra-software-to-install' multiply defined Label `Install:fedora-centos-and-rhel' multiply defined Label `Install:frequently-encountered-problems' multiply defined Label `Install:how-to-build-from-source-with-conda' multiply defined Label `Install:how-to-get-conda' multiply defined Label `Install:how-to-install-rdkit-with-conda' multiply defined Label `Install:installation' multiply defined Label `Install:installation-from-repositories' multiply defined Label `Install:installation-from-source' multiply defined Label `Install:installation-of-rdkit-binaries' multiply defined Label `Install:installing-and-using-postgresql-and-the-rdkit-postgresql-cartridge-from-a-conda-environment' multiply defined Label `Install:installing-boost' multiply defined Label `Install:installing-prerequisites-from-source' multiply defined Label `Install:introduction-to-anaconda' multiply defined Label `Install:license' multiply defined Label `Install:linux-and-os-x' multiply defined Label `Install:linux-x86-64-python-3-environment' multiply defined Label `Install:macos-10-12-sierra-python-3-environment' multiply defined Label `Install:optional-packages' multiply defined Label `Install:os-x' multiply defined Label `Install:prerequisites' multiply defined Label `Install:recommended-extras' multiply defined Label `Install:setup-and-preparation' multiply defined Label `Install:specifying-an-alternate-boost-installation' multiply defined Label `Install:specifying-an-alternate-python-installation' multiply defined Label `Install:testing-the-build-optional-but-recommended' multiply defined Label `Install:ubuntu-12-04-and-later' multiply defined Label `Install:windows' multiply defined Label `Overview:an-overview-of-the-rdkit' multiply defined Label `Overview:footnotes' multiply defined Label `Overview:history' multiply defined Label `Overview:integration-with-other-open-source-projects' multiply defined Label `Overview:license' multiply defined Label `Overview:open-source-toolkit-for-cheminformatics' multiply defined Label `Overview:operational' multiply defined Label `Overview:the-contrib-directory' multiply defined Label `Overview:usage-by-other-open-source-projects' multiply defined Label `Overview:what-is-it' multiply defined Latexmk: Summary of warnings from last run of (pdf)latex: Latex found 114 multiply defined reference(s) === TeX engine is 'pdfTeX' Latexmk: All targets (RDKit.pdf) are up-to-date make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/Docs/Book/_build/latex' pdflatex finished; the PDF files are in _build/latex. make[2]: Leaving directory '/build/rdkit-201809.1+dfsg/Docs/Book' make[1]: Leaving directory '/build/rdkit-201809.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/rdkit-201809.1+dfsg' cp -r rdkit obj-*/ find /build/rdkit-201809.1+dfsg -name rdchem.so /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/rdchem.so #export RDBASE=/build/rdkit-201809.1+dfsg PYTHONPATH=/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/ LD_LIBRARY_PATH="/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf//lib:" PYTHONPATH=/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/:/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf//rdkit/Chem/ LD_LIBRARY_PATH="/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf//lib:" dh_auto_test cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=-j4 make[2]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Running tests... /usr/bin/ctest --force-new-ctest-process -j4 Test project /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf Start 1: testDict Start 2: testRDValue Start 3: testDataStructs Start 4: testFPB 1/142 Test #2: testRDValue ........................ Passed 0.13 sec Start 5: testMultiFPB 2/142 Test #4: testFPB ............................ Passed 0.17 sec Start 6: pyBV 3/142 Test #3: testDataStructs .................... Passed 0.25 sec Start 7: pyDiscreteValueVect 4/142 Test #5: testMultiFPB ....................... Passed 0.29 sec Start 8: pySparseIntVect 5/142 Test #8: pySparseIntVect .................... Passed 4.11 sec Start 9: pyFPB 6/142 Test #7: pyDiscreteValueVect ................ Passed 4.46 sec Start 10: testTransforms 7/142 Test #10: testTransforms ..................... Passed 0.18 sec Start 11: testGrid 8/142 Test #11: testGrid ........................... Passed 1.02 sec Start 12: testPyGeometry 9/142 Test #9: pyFPB .............................. Passed 3.62 sec Start 13: testMatrices 10/142 Test #13: testMatrices ....................... Passed 0.11 sec Start 14: testAlignment 11/142 Test #14: testAlignment ...................... Passed 0.16 sec Start 15: pyAlignment 12/142 Test #12: testPyGeometry ..................... Passed 4.75 sec Start 16: testOptimizer 13/142 Test #16: testOptimizer ...................... Passed 0.34 sec Start 17: testUFFForceField 14/142 Test #15: pyAlignment ........................ Passed 3.67 sec Start 18: testMMFFForceField 15/142 Test #17: testUFFForceField .................. Passed 2.32 sec Start 19: pyForceFieldConstraints 16/142 Test #6: pyBV ............................... Passed 22.96 sec Start 20: testDistGeom 17/142 Test #20: testDistGeom ....................... Passed 0.30 sec Start 21: pyDistGeom 18/142 Test #19: pyForceFieldConstraints ............ Passed 10.44 sec Start 22: graphmolTest1 19/142 Test #21: pyDistGeom ......................... Passed 4.02 sec Start 23: graphmolcpTest 20/142 Test #23: graphmolcpTest ..................... Passed 0.60 sec Start 24: graphmolqueryTest 21/142 Test #24: graphmolqueryTest .................. Passed 0.59 sec Start 25: graphmolMolOpsTest 22/142 Test #1: testDict ........................... Passed 33.44 sec Start 26: graphmoltestCanon 23/142 Test #26: graphmoltestCanon .................. Passed 0.26 sec Start 27: graphmoltestChirality 24/142 Test #27: graphmoltestChirality .............. Passed 1.57 sec Start 28: graphmoltestPickler 25/142 Test #28: graphmoltestPickler ................Child aborted***Exception: 7.89 sec [11:29:49] ------------------------------------- [11:29:49] Testing String Pickle Roundtrips. [11:29:50] done [11:29:50] ------------------------------------- [11:29:50] Testing reading existing pickle file (v2). [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing combining molecules using pickles. Atoms: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 Bonds: 0 0->1 order: 1 conj?: 0 aromatic?: 0 1 1->2 order: 1 conj?: 0 aromatic?: 0 2 2->0 order: 1 conj?: 0 aromatic?: 0 3 3->4 order: 1 conj?: 0 aromatic?: 0 4 4->5 order: 1 conj?: 0 aromatic?: 0 5 5->6 order: 1 conj?: 0 aromatic?: 0 6 6->3 order: 1 conj?: 0 aromatic?: 0 [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing Issue164: Roundtrip Pickle Failure. [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing Issue219: Pickle Failure with Conformations. [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing Issue220: Pickle problems with bond stereochemistry. [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing query serialization. [11:29:52] C=[$(C=O)] [11:29:52] S(=O)(=O)-[C&H2]-,:[F,Br,I,Cl] S(=O)(=O)-[C&H2]-,:[F,Br,I,Cl] [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing radical handling in pickles. [11:29:52] done [11:29:52] ----------------------- [11:29:52] Testing pickling of properties [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing sf.net issue 2788233. [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing sf.net issue 3202580. mass! 13.0034 [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing sf.net issue 3316407. [11:29:52] done [11:29:52] ------------------------------------- [11:29:52] Testing sf.net issue 3496759. smi match: *C *C smi match: **=* **=* smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O smi match: *OS(=O)OC *OS(=O)OC smi match: *S(=O)(=O)OC *S(=O)(=O)OC smi match: O=COC=O O=COC=O smi match: OO OO smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 smi match: nnnOC=O nnnOC=O smi match: *=C=N *=C=N smi match: O=S(=O)(O)C(F)(F)F O=S(=O)(O)C(F)(F)F smi match: S=[PH](S)S S=[PH](S)S smi match: NP(N)(N)=O NP(N)(N)=O smi match: cN=[N+]=[N-] cN=[N+]=[N-] smi match: *CC=O *CC=O smi match: NNC=O NNC=O smi match: * * smi match: C=P C=P smi match: CC(=N)Cl CC(=N)Cl smi match: N=O N=O smi match: ** ** smi match: N=C=N N=C=N smi match: [C-]#[NH+] [C-]#[NH+] smi match: O=CON(C=O)C=O O=CON(C=O)C=O smi match: N#CCO N#CCO smi match: N#CC=O N#CC=O smi match: N#C[SH](=O)=O N#C[SH](=O)=O smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC smi match: N#CN=N N#CN=N smi match: N=NCC=O N=NCC=O smi match: CCCCCCC CCCCCCC smi match: OCCOCCO OCCOCCO smi match: SS SS smi match: [SH] [SH] smi match: *1CC1 *1CC1 smi match: Occc(O)cO Occc(O)cO smi match: Occ(O)cO Occ(O)cO smi match: N=NC(N)=S N=NC(N)=S smi match: N#CS N#CS smi match: cC[NH3+] cC[NH3+] smi match: C*C=S C*C=S smi match: N#CCN N#CCN smi match: O=C1CCO1 O=C1CCO1 smi match: O=[PH](O)O[PH](=O)O O=[PH](O)O[PH](=O)O smi match: O=C1CCN1 O=C1CCN1 smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 smi match: C=CC=CC=CC=C C=CC=CC=CC=C smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 smi match: O=C1NCC2CCCCC12 O=C1NCC2CCCCC12 smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 smi match: Oc1cc(O)c2c(c1)OC(c1ccc(O)c(O)c1)C(O)C2 Oc1cc(O)c2c(c1)OC(c1ccc(O)c(O)c1)C(O)C2 smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 smi match: cN(=O)~O cN(=O)~O smi match: *CN1C(=O)CCC1=O *CN1C(=O)CCC1=O smi match: N~NC=O N~NC=O smi match: *=N~C *=N~C smi match: CO*(=O)=O CO*(=O)=O smi match: * * smi match: * * smi match: *C=C *C=C smi match: N#CS N#CS smi match: *C=S *C=S smi match: *N *N smi match: *C(=C)C=O *C(=C)C=O smi match: *C#C *C#C smi match: N#CCO N#CCO smi match: O=N(=O)CCO O=N(=O)CCO smi match: N=CS N=CS smi match: O=CNC(O)C=O O=CNC(O)C=O smi match: C=C(C=O)C=O C=C(C=O)C=O smi match: N=CC=O N=CC=O smi match: *C(C=O)C=O *C(C=O)C=O smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O smi match: O=CC=CC=O O=CC=CC=O smi match: O=CN(O)C=O O=CN(O)C=O smi match: O=CN(S)C=O O=CN(S)C=O smi match: O=CNC=O O=CNC=O smi match: O=CNN=O O=CNN=O smi match: O=CNNC=O O=CNNC=O smi match: O=CNOC=O O=CNOC=O smi match: O=CS O=CS smi match: O=CSC=S O=CSC=S smi match: S=CS S=CS smi match: C=O C=O smi match: *C=N *C=N smi match: CCCCCCC CCCCCCC smi match: CN=O CN=O smi match: CS(=O)(=O)O CS(=O)(=O)O smi match: O=C1CCO1 O=C1CCO1 smi match: C=C(S)[SH]=O C=C(S)[SH]=O smi match: C=CCO C=CCO smi match: C=CC=N C=CC=N smi match: C=CC=O C=CC=O smi match: C=CC(=O)C=C C=CC(=O)C=C smi match: C=CC=S C=CC=S smi match: C=CC(=S)S C=CC(=S)S smi match: *C=C(*)C=C *C=C(*)C=C smi match: C=CC=N C=CC=N smi match: *N(*)C=C *N(*)C=C smi match: C=CN(=O)=O C=CN(=O)=O smi match: C=CN(=O)O C=CN(=O)O smi match: C=CO C=CO smi match: C=COC=O C=COC=O smi match: C=CS C=CS smi match: C=C[SH](=O)=O C=C[SH](=O)=O smi match: C=NCO C=NCO smi match: C=NC=O C=NC=O smi match: C=NN C=NN smi match: C=NN=C C=NN=C smi match: C=NO C=NO smi match: C=NOC=O C=NOC=O smi match: C=N=O C=N=O smi match: N#CS N#CS smi match: *CN=O *CN=O smi match: NCN NCN smi match: O=NCC=NO O=NCC=NO smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O smi match: N=C(N)S N=C(N)S smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 smi match: NC=S NC=S smi match: NC(N)=S NC(N)=S smi match: C=CN C=CN smi match: NOC=O NOC=O smi match: C1CN1 C1CN1 smi match: O=C1NNNN1 O=C1NNNN1 smi match: N=C(N)C(=N)N N=C(N)C(=N)N smi match: N=C(N)O N=C(N)O smi match: N=C(N)C(=N)S N=C(N)C(=N)S smi match: *C=N *C=N smi match: N=CC=O N=CC=O smi match: N=CS N=CS smi match: N=C=N N=C=N smi match: N=C=O N=C=O smi match: N=C=S N=C=S smi match: NOC(=O)O NOC(=O)O smi match: *C(O)=S *C(O)=S smi match: C=CO C=CO smi match: ON=CC=NO ON=CC=NO smi match: *C[SH](=O)=O *C[SH](=O)=O smi match: O=[SH](=O)O O=[SH](=O)O smi match: N#CS N#CS smi match: C=C(S)S C=C(S)S smi match: N=C(N)S N=C(N)S smi match: N=C(S)S N=C(S)S smi match: NC(=S)S NC(=S)S smi match: O=CNS O=CNS smi match: S S smi match: [SiH4] [SiH4] smi match: NS NS smi match: NCN NCN smi match: cC(c)(O)O cC(c)(O)O smi match: *C(c)O *C(c)O smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O smi match: cS(=O)(=O)O cS(=O)(=O)O smi match: *c1ccccn1=O *c1ccccn1=O smi match: *c1ccccn1 *c1ccccn1 smi match: *c1nccccn1 *c1nccccn1 smi match: C1COCOC1 C1COCOC1 smi match: C=S C=S smi match: c=S c=S smi match: S=CS S=CS smi match: C=CN(=O)=O C=CN(=O)=O smi match: C=CN(=O)O C=CN(=O)O smi match: N=CC=O N=CC=O smi match: C=CS C=CS smi match: SC(S)(S)S SC(S)(S)S smi match: OS(O)(O)O OS(O)(O)O smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O smi match: N#CS N#CS smi match: C=NO C=NO smi match: C=N[SH]=N C=N[SH]=N smi match: O=C(S)S O=C(S)S smi match: N=C(S)S N=C(S)S smi match: N=C(=N)S N=C(=N)S smi match: O=N=O O=N=O smi match: O=NO O=NO smi match: ONO ONO smi match: C1SCS1 C1SCS1 smi match: N=C=S N=C=S smi match: N=C=N N=C=N smi match: C1N=N1 C1N=N1 smi match: *CS *CS smi match: SC(S)=C(S)S SC(S)=C(S)S smi match: N=CC=NO N=CC=NO smi match: N#CCC#N N#CCC#N smi match: CON=O CON=O smi match: C=CN C=CN smi match: C=N[SH](=O)=O C=N[SH](=O)=O smi match: NN=O NN=O smi match: NC(=O)S NC(=O)S smi match: N#CS N#CS smi match: NC(=O)C(N)=O NC(=O)C(N)=O smi match: c=N c=N smi match: C1COCO1 C1COCO1 smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O smi match: O=CC=O O=CC=O smi match: O=CNOC=O O=CNOC=O smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 smi match: ONO ONO smi match: ON(~O)~O ON(~O)~O smi match: OC1COC(O)C1 OC1COC(O)C1 smi match: OC1CCOC1O OC1CCOC1O smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 smi match: N=[N+]=N N=[N+]=N smi match: N#CN N#CN smi match: C=NN=C C=NN=C smi match: *CCN(C)C *CCN(C)C smi match: CNN CNN smi match: *CC *CC smi match: OCS OCS smi match: C1NO1 C1NO1 smi match: COS(C)(=O)=O COS(C)(=O)=O smi match: C1CO1 C1CO1 smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 smi match: *C(*)=C *C(*)=C smi match: N#[NH+] N#[NH+] smi match: C#NO C#NO smi match: OOO OOO smi match: OO OO smi match: O~Cl(~O)~O O~Cl(~O)~O smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O smi match: [OH]~C(~O)~O [OH]~C(~O)~O smi match: *N *N smi match: *P *P smi match: *S *S smi match: *C(*)(*)C=C *C(*)(*)C=C smi match: *C(*)(*)C=C *C(*)(*)C=C smi match: *C(*)C=C *C(*)C=C smi match: *CC=C *CC=C smi match: CN=C=O CN=C=O smi match: CN=C=S CN=C=S smi match: *C=O *C=O smi match: N=N N=N smi match: SS SS smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 smi match: CSC(C)=N CSC(C)=N smi match: COC(C)=N COC(C)=N smi match: C=C=C C=C=C smi match: *C(=O)OC=O *C(=O)OC=O smi match: C=CC#N C=CC#N smi match: C=CC=O C=CC=O smi match: CC=CC(C)=O CC=CC(C)=O smi match: CC=CC(=O)OCC CC=CC(=O)OCC smi match: C#CC#N C#CC#N smi match: C#CC=O C#CC=O smi match: C#CC(=O)OCC C#CC(=O)OCC smi match: C#CC=O C#CC=O smi match: *C(=O)C#C *C(=O)C#C smi match: C=CC=O C=CC=O smi match: *C(*)(*)O *C(*)(*)O smi match: COS(=O)(=O)O COS(=O)(=O)O smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] smi match: *C(*)(*)C=O *C(*)(*)C=O smi match: *C(*)(*)C=O *C(*)(*)C=O smi match: *C(*)C=O *C(*)C=O smi match: *CC=O *CC=O smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O smi match: *C[SH](=O)=O *C[SH](=O)=O smi match: * * smi match: *1CC1 *1CC1 smi match: O=COC=O O=COC=O smi match: N=C=O N=C=O smi match: N=C=S N=C=S smi match: O~O O~O smi match: N~[SiH4] N~[SiH4] smi match: *P *P smi match: C=N=N C=N=N smi match: *N#[NH+] *N#[NH+] smi match: *S* *S* smi match: ** ** smi match: *CC* *CC* smi match: *O[SiH3] *O[SiH3] smi match: *OS(*)~O *OS(*)~O smi match: N~N~O N~N~O smi match: *N(~O)(~O)~O *N(~O)(~O)~O smi match: *[N+](=C)[O-] *[N+](=C)[O-] smi match: * * smi match: *C(*)NCN(*)* *C(*)NCN(*)* smi match: *OCC#N *OCC#N smi match: **C=C **C=C smi match: C=C[O-] C=C[O-] smi match: C=CO C=CO smi match: * * smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O smi match: O=COn1ccnc1 O=COn1ccnc1 smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F smi match: CC(C)(C)S CC(C)(C)S 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 smi match: [CH]=O [CH]=O smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C smi match: SS SS smi match: [SH] [SH] smi match: *C* *C* smi match: * * smi match: C[nH3+] C[nH3+] smi match: cC(=N)N cC(=N)N smi match: O=CNO O=CNO smi match: NN NN smi match: * * smi match: *O[PH](=O)O* *O[PH](=O)O* smi match: * * smi match: * * smi match: * * smi match: *N=C(*)* *N=C(*)* smi match: *C(*)(*)C=O *C(*)(*)C=O smi match: CSC=O CSC=O smi match: * * smi match: O=CCl O=CCl smi match: *** *** smi match: *C=O *C=O smi match: CO CO smi match: CO CO smi match: CO CO smi match: CO CO smi match: CC=O CC=O smi match: *=* *=* smi match: *C *C smi match: C#C C#C smi match: *[CH]C=C *[CH]C=C smi match: cCC(=O)O cCC(=O)O smi match: *C(*)(*)C(=O)O *C(*)(*)C(=O)O smi match: CC(=O)C(=O)O CC(=O)C(=O)O smi match: C=CC(=O)O C=CC(=O)O smi match: N#CC(=O)O N#CC(=O)O smi match: O=C(O)CN(~O)~O O=C(O)CN(~O)~O smi match: *N(*)C*=O *N(*)C*=O smi match: O=*CO O=*CO smi match: *=C*=O *=C*=O smi match: *=CC#N *=CC#N smi match: *CO *CO smi match: ** ** smi match: *CO *CO smi match: *C(*)=O *C(*)=O smi match: * * smi match: *CC(=O)O *CC(=O)O smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O smi match: *c *c smi match: cN(C)C cN(C)C smi match: c c smi match: *c *c smi match: *c *c smi match: **:*cF **:*cF smi match: cB(O)O cB(O)O smi match: N~N~N N~N~N smi match: *N=N* *N=N* smi match: *CCO *CCO smi match: *CCO *CCO smi match: *=CCC(=O)O *=CCC(=O)O smi match: O=C(O)CCO O=C(O)CCO smi match: *CCC(=O)O *CCC(=O)O smi match: CC(=O)CC(=O)O CC(=O)CC(=O)O smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O smi match: *OC(*)=O *OC(*)=O smi match: *C(=O)O *C(=O)O smi match: O=CO O=CO smi match: *OC(=O)O* *OC(=O)O* smi match: * * smi match: *OC(=O)Cl *OC(=O)Cl smi match: *C#N *C#N smi match: NCC(=O)NCC=O NCC(=O)NCC=O smi match: SS SS smi match: * * smi match: *=* *=* smi match: *=* *=* smi match: *=* *=* smi match: *=* *=* smi match: C1CO1 C1CO1 smi match: *OC(*)=O *OC(*)=O smi match: * * smi match: *O*O *O*O smi match: COC(C)(C)O COC(C)(C)O smi match: *O *O smi match: ** ** smi match: C=NN C=NN smi match: C=NC=O C=NC=O smi match: * * smi match: C#NC C#NC smi match: CN=C=O CN=C=O smi match: CN=C=S CN=C=S smi match: *OC(*)(*)O* *OC(*)(*)O* smi match: *C(*)=O *C(*)=O smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C smi match: *~*=O *~*=O smi match: *~*=O *~*=O smi match: O=C(O)CC(=O)O O=C(O)CC(=O)O smi match: * * smi match: *C#N *C#N smi match: *N(=O)~O *N(=O)~O smi match: N N smi match: O=C(O)C(=O)O O=C(O)C(=O)O smi match: C=NO C=NO smi match: O~O O~O smi match: cO cO smi match: O=P(~[OH])~O O=P(~[OH])~O smi match: CO~P(=O)~O CO~P(=O)~O smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O smi match: O=P(~O)~O O=P(~O)~O smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O smi match: CN CN smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 smi match: * * smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 smi match: CS(C)~O CS(C)~O smi match: CS(C)(~O)~O CS(C)(~O)~O smi match: CS(N)(~O)~O CS(N)(~O)~O smi match: CS(O)(~O)~O CS(O)(~O)~O smi match: COS(C)(~O)~O COS(C)(~O)~O smi match: *S(C)(~O)~O *S(C)(~O)~O smi match: CN(C)C CN(C)C smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 smi match: *C(*)=S *C(*)=S smi match: *OC(*)=S *OC(*)=S smi match: * * smi match: CS CS smi match: cS cS smi match: NC(N)=S NC(N)=S smi match: * * smi match: ***** ***** smi match: NC(N)=O NC(N)=O [11:29:56] done [11:29:56] ------------------------------------- [11:29:56] Testing sf.net issue 280. [11:29:56] done [11:29:56] ------------------------------------- [11:29:56] Testing sf.net issue 285. [11:29:56] done [11:29:56] ----------------------- [11:29:56] Testing residue information handling on atoms [11:29:56] done [11:29:56] ----------------------- [11:29:56] Testing Github issue 149: cannot pickle unsanitized molecules [11:29:56] done [11:29:56] ----------------------- [11:29:56] Testing Github issue 713: Molecule serialization doesn't read/write atomic numbers above 128 [11:29:56] done [11:29:56] ----------------------- [11:29:56] Testing Github 1563: Add a canned Atom query for heavy atom degree [11:29:56] done [11:29:56] ----------------------- [11:29:56] Testing Github 1710: bonds that are STEREOCIS or STEREOTRANS cannot be depickled [11:29:56] done [11:29:56] ----------------------- [11:29:56] Testing Github 1999: pickling atom map numbers >127 gives negative values terminate called after throwing an instance of 'RDKit::MolPicklerException' what(): std::exception Start 29: graphmoltestPicklerGlobalSetting 26/142 Test #29: graphmoltestPicklerGlobalSetting ... Passed 0.55 sec Start 30: graphmolIterTest 27/142 Test #30: graphmolIterTest ................... Passed 0.50 sec Start 31: hanoiTest 28/142 Test #25: graphmolMolOpsTest ................. Passed 59.31 sec Start 32: graphmolMemTest1 29/142 Test #32: graphmolMemTest1 ................... Passed 0.24 sec Start 33: resMolSupplierTest 30/142 Test #33: resMolSupplierTest ................. Passed 19.31 sec Start 34: molBundleTest 31/142 Test #34: molBundleTest ...................... Passed 0.58 sec Start 35: test-valgrind 32/142 Test #35: test-valgrind ...................... Passed 0.52 sec Start 36: graphmolTestsCatch 33/142 Test #36: graphmolTestsCatch ................. Passed 0.62 sec Start 37: testDepictor 34/142 Test #37: testDepictor ....................... Passed 8.51 sec Start 38: pyDepictor 35/142 Test #38: pyDepictor ......................... Passed 11.60 sec Start 39: smiTest1 36/142 Test #39: smiTest1 ........................... Passed 0.61 sec Start 40: smiTest2 37/142 Test #40: smiTest2 ........................... Passed 0.18 sec Start 41: cxsmilesTest 38/142 Test #41: cxsmilesTest ....................... Passed 0.47 sec Start 42: smaTest1 39/142 Test #42: smaTest1 ........................... Passed 4.86 sec Start 43: smiTestCatch 40/142 Test #43: smiTestCatch ....................... Passed 0.67 sec Start 44: fileParsersTest1 41/142 Test #44: fileParsersTest1 ................... Passed 1.21 sec Start 45: testMolSupplier 42/142 Test #45: testMolSupplier .................... Passed 4.11 sec Start 46: testMolWriter 43/142 Test #46: testMolWriter ...................... Passed 5.33 sec Start 47: testTplParser 44/142 Test #47: testTplParser ...................... Passed 0.55 sec Start 48: testMol2ToMol 45/142 Test #48: testMol2ToMol ...................... Passed 0.73 sec Start 49: testSequence 46/142 Test #49: testSequence ....................... Passed 0.81 sec Start 50: testExtendedStereoParsing 47/142 Test #50: testExtendedStereoParsing .......... Passed 0.48 sec Start 51: fileParsersCatchTest 48/142 Test #51: fileParsersCatchTest ............... Passed 0.49 sec Start 52: testSubstructMatch 49/142 Test #52: testSubstructMatch ................. Passed 10.98 sec Start 53: testReaction 50/142 Test #53: testReaction ....................... Passed 6.67 sec Start 54: testReactionFingerprints 51/142 Test #54: testReactionFingerprints ........... Passed 1.07 sec Start 55: testEnumeration 52/142 Test #18: testMMFFForceField ................. Passed 592.45 sec Start 56: rxnTestCatch 53/142 Test #56: rxnTestCatch ....................... Passed 1.20 sec Start 57: pyChemReactions 54/142 Test #57: pyChemReactions .................... Passed 11.85 sec Start 58: pyChemReactionEnumerations 55/142 Test #55: testEnumeration .................... Passed 449.54 sec Start 59: pyChemReactionSanitize 56/142 Test #59: pyChemReactionSanitize ............. Passed 5.96 sec Start 60: testChemTransforms 57/142 Test #60: testChemTransforms ................. Passed 2.27 sec Start 61: testSubgraphs1 58/142 Test #61: testSubgraphs1 ..................... Passed 6.45 sec Start 62: testSubgraphs2 59/142 Test #62: testSubgraphs2 ..................... Passed 0.57 sec Start 63: filterCatalogTest 60/142 Test #63: filterCatalogTest .................. Passed 3.20 sec Start 64: pyFilterCatalog 61/142 Test #64: pyFilterCatalog .................... Passed 46.45 sec Start 65: testFragCatalog 62/142 Test #58: pyChemReactionEnumerations ......... Passed 80.86 sec Start 66: pyFragCatalog 63/142 Test #66: pyFragCatalog ...................... Passed 6.73 sec Start 67: testDescriptors 64/142 Test #65: testFragCatalog .................... Passed 24.28 sec Start 68: testAUTOCORR2D 65/142 Test #68: testAUTOCORR2D ..................... Passed 9.20 sec Start 69: pyMolDescriptors 66/142 Test #69: pyMolDescriptors ................... Passed 7.28 sec Start 70: pyMolDescriptors3D 67/142 Test #70: pyMolDescriptors3D ................. Passed 4.92 sec Start 71: testFingerprints 68/142 Test #67: testDescriptors .................... Passed 83.56 sec Start 72: testFingerprintGenerators 69/142 Test #72: testFingerprintGenerators .......... Passed 21.31 sec Start 73: pyTestGenerator 70/142 Test #73: pyTestGenerator .................... Passed 3.74 sec Start 74: testPartialCharges 71/142 Test #74: testPartialCharges ................. Passed 0.40 sec Start 75: pyPartialCharges 72/142 Test #31: hanoiTest .......................... Passed 773.31 sec Start 76: testMolTransforms 73/142 Test #76: testMolTransforms .................. Passed 0.53 sec Start 77: pyMolTransforms 74/142 Test #75: pyPartialCharges ................... Passed 6.47 sec Start 78: testMMFFForceFieldHelpers 75/142 Test #77: pyMolTransforms .................... Passed 4.56 sec Start 79: testUFFForceFieldHelpers 76/142 Test #71: testFingerprints ................... Passed 140.50 sec Start 80: testCrystalForceField 77/142 Test #80: testCrystalForceField .............. Passed 1.38 sec Start 81: pyForceFieldHelpers 78/142 Test #81: pyForceFieldHelpers ................ Passed 8.97 sec Start 82: testDistGeomHelpers 79/142 Test #78: testMMFFForceFieldHelpers .......... Passed 426.37 sec Start 83: pyDistGeomHelpers 80/142 Test #79: testUFFForceFieldHelpers ........... Passed 484.79 sec Start 84: testMolAlign 81/142 Test #22: graphmolTest1 ...................... Passed 2109.86 sec Start 85: pyMolAlign 82/142 Test #83: pyDistGeomHelpers .................. Passed 1029.38 sec Start 86: testFeatures 83/142 Test #86: testFeatures ....................... Passed 1.24 sec Start 87: pyChemicalFeatures 84/142 Test #87: pyChemicalFeatures ................. Passed 8.70 sec Start 88: testShapeHelpers 85/142 Test #88: testShapeHelpers ................... Passed 0.69 sec Start 89: pyShapeHelpers 86/142 Test #89: pyShapeHelpers ..................... Passed 6.33 sec Start 90: testMolCatalog 87/142 Test #90: testMolCatalog ..................... Passed 0.52 sec Start 91: pyMolCatalog 88/142 Test #91: pyMolCatalog ....................... Passed 4.99 sec Start 92: moldraw2DTest1 89/142 Test #92: moldraw2DTest1 ..................... Passed 113.52 sec Start 93: moldraw2DRxnTest1 90/142 Test #93: moldraw2DRxnTest1 .................. Passed 2.44 sec Start 94: pyMolDraw2D 91/142 Test #94: pyMolDraw2D ........................ Passed 9.62 sec Start 95: testFMCS 92/142 Test #95: testFMCS ........................... Passed 24.33 sec Start 96: pyFMCS 93/142 Test #96: pyFMCS ............................. Passed 26.03 sec Start 97: FMCStest 94/142 Test #97: FMCStest ........................... Passed 0.68 sec Start 98: testMolHash 95/142 Test #98: testMolHash ........................ Passed 2.50 sec Start 99: pyMolHash 96/142 Test #99: pyMolHash .......................... Passed 6.17 sec Start 100: testMMPA 97/142 Test #100: testMMPA ........................... Passed 3.96 sec Start 101: pyMMPA 98/142 Test #101: pyMMPA ............................. Passed 119.17 sec Start 102: testStructChecker 99/142 Test #102: testStructChecker .................. Passed 3.20 sec Start 103: pyStructChecker 100/142 Test #103: pyStructChecker .................... Passed 5.02 sec Start 104: testReducedGraphs 101/142 Test #104: testReducedGraphs .................. Passed 1.48 sec Start 105: pyReducedGraphs 102/142 Test #105: pyReducedGraphs .................... Passed 9.07 sec Start 106: trajectoryTest 103/142 Test #85: pyMolAlign ......................... Passed 496.55 sec Start 107: substructLibraryTest 104/142 Test #107: substructLibraryTest ............... Passed 17.25 sec Start 108: pySubstructLibrary 105/142 Test #106: trajectoryTest ..................... Passed 24.24 sec Start 109: testRGroupDecomp 106/142 Test #109: testRGroupDecomp ................... Passed 6.36 sec Start 110: pyRGroupDecomposition 107/142 Test #110: pyRGroupDecomposition .............. Passed 13.05 sec Start 111: molInterchangeTest1 108/142 Test #111: molInterchangeTest1 ................ Passed 0.84 sec Start 112: pyMolInterchange 109/142 Test #112: pyMolInterchange ................... Passed 9.66 sec Start 113: testSLNParse 110/142 Test #113: testSLNParse ....................... Passed 3.49 sec Start 114: pySLNParse 111/142 Test #114: pySLNParse ......................... Passed 16.84 sec Start 115: pyGraphMolWrap 112/142 Test #108: pySubstructLibrary ................. Passed 111.34 sec Start 116: pyTestConformerWrap 113/142 Test #116: pyTestConformerWrap ................ Passed 14.31 sec Start 117: pyTestTrajectory 114/142 Test #117: pyTestTrajectory ................... Passed 28.64 sec Start 118: pyTestThreads 115/142 Test #118: pyTestThreads ...................... Passed 13.40 sec Start 119: molStandardizeTest 116/142 Test #119: molStandardizeTest ................. Passed 8.52 sec Start 120: molNormalizeTest 117/142 Test #120: molNormalizeTest ................... Passed 1.04 sec Start 121: molValidateTest 118/142 Test #121: molValidateTest .................... Passed 2.52 sec Start 122: molChargeTest 119/142 Test #122: molChargeTest ...................... Passed 4.10 sec Start 123: molTautomerTest 120/142 Test #123: molTautomerTest .................... Passed 83.37 sec Start 124: molStandardizeSmallTest 121/142 Test #124: molStandardizeSmallTest ............ Passed 1.66 sec Start 125: molFragmentTest 122/142 Test #125: molFragmentTest .................... Passed 4.11 sec Start 126: pyMolStandardize 123/142 Test #126: pyMolStandardize ................... Passed 13.21 sec Start 127: testQuery 124/142 Test #127: testQuery .......................... Passed 0.15 sec Start 128: testMatCalc 125/142 Test #128: testMatCalc ........................ Passed 0.06 sec Start 129: pyMatCalc 126/142 Test #129: pyMatCalc .......................... Passed 29.39 sec Start 130: testSimDivPickers 127/142 Test #130: testSimDivPickers .................. Passed 0.15 sec Start 131: pySimDivPickers 128/142 Test #131: pySimDivPickers .................... Passed 14.73 sec Start 132: pyRanker 129/142 Test #132: pyRanker ........................... Passed 8.79 sec Start 133: testChemicalFeatures 130/142 Test #133: testChemicalFeatures ............... Passed 0.12 sec Start 134: pyFeatures 131/142 Test #134: pyFeatures ......................... Passed 6.20 sec Start 135: pythonTestDbCLI 132/142 Test #115: pyGraphMolWrap ..................... Passed 574.82 sec Start 136: pythonTestDirML 133/142 Test #135: pythonTestDbCLI .................... Passed 517.60 sec Start 137: pythonTestDirDataStructs 134/142 Test #137: pythonTestDirDataStructs ........... Passed 15.13 sec Start 138: pythonTestDirDbase 135/142 Test #138: pythonTestDirDbase ................. Passed 7.91 sec Start 139: pythonTestDirSimDivFilters 136/142 Test #139: pythonTestDirSimDivFilters ......... Passed 6.58 sec Start 140: pythonTestDirVLib 137/142 Test #140: pythonTestDirVLib .................. Passed 11.83 sec Start 141: pythonTestDirChem 138/142 Test #136: pythonTestDirML .................... Passed 315.18 sec Start 142: pythonTestSping 139/142 Test #142: pythonTestSping .................... Passed 11.08 sec 140/142 Test #84: testMolAlign ....................... Passed 2556.46 sec 141/142 Test #82: testDistGeomHelpers ................ Passed 3149.70 sec 142/142 Test #141: pythonTestDirChem ..................***Failed 2356.76 sec ...... ---------------------------------------------------------------------- Ran 6 tests in 1.743s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.752s OK ....[12:28:42] **** Pre-condition Violation valence not defined for atoms not associated with molecules Violation occurred on line 266 in file ./Code/GraphMol/Atom.cpp Failed Expression: dp_mol **** . ---------------------------------------------------------------------- Ran 5 tests in 0.173s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.170s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.171s OK ...................... ---------------------------------------------------------------------- Ran 22 tests in 0.588s OK .....s.................ss ---------------------------------------------------------------------- Ran 25 tests in 2.281s OK (skipped=3) ..s ---------------------------------------------------------------------- Ran 3 tests in 5.832s OK (skipped=1) ..............................F.... ====================================================================== FAIL: test_timeout (__main__.TestTimeout) ---------------------------------------------------------------------- Traceback (most recent call last): File "UnitTestMCS.py", line 331, in test_timeout self.assertTrue(t2 - t1 < 2, t2 - t1) AssertionError: 15.5066452026 ---------------------------------------------------------------------- Ran 35 tests in 16.210s FAILED (failures=1) .... ---------------------------------------------------------------------- Ran 4 tests in 0.518s OK . ---------------------------------------------------------------------- Ran 1 test in 0.364s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 1.230s OK ... ---------------------------------------------------------------------- Ran 3 tests in 1.325s OK .ss.ss....... ---------------------------------------------------------------------- Ran 13 tests in 35.337s OK (skipped=4) ........F...[12:41:09] WARNING: More than one matching pattern found - picking one [12:41:09] WARNING: More than one matching pattern found - picking one .[12:41:11] WARNING: More than one matching pattern found - picking one .. ====================================================================== FAIL: testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable (__main__.TestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "UnitTestMol3D.py", line 218, in testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable self.assertEqual(smiles, expected) AssertionError: Items in the first set but not the second: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@@H](N)I' 'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@@H](N)I' Items in the second set but not the first: 'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I' 'C/C(F)=C/[C@H](Cl)/C=C(\\Br)[C@H](N)I' ---------------------------------------------------------------------- Ran 15 tests in 637.860s FAILED (failures=1) ........ ---------------------------------------------------------------------- Ran 8 tests in 2.829s OK ....[12:42:55] WARNING: not removing hydrogen atom without neighbors [12:42:55] WARNING: not removing hydrogen atom without neighbors [12:42:55] WARNING: not removing hydrogen atom without neighbors ....... ---------------------------------------------------------------------- Ran 11 tests in 91.546s OK .... ---------------------------------------------------------------------- Ran 4 tests in 30.528s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 9.057s OK ...............s/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/PandasTools.py:394: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. if (np.issubdtype(df.dtypes[dt], float) or np.issubdtype(df.dtypes[dt], int)) /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/PandasTools.py:394: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. if (np.issubdtype(df.dtypes[dt], float) or np.issubdtype(df.dtypes[dt], int)) ./build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/PandasTools.py:414: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. if np.issubdtype(type(cell_value), float): ....... ---------------------------------------------------------------------- Ran 24 tests in 97.077s OK (skipped=1) .. ---------------------------------------------------------------------- Ran 2 tests in 0.013s OK UnitTestDocTestsChem.py:5: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead. from rdkit.Chem import MCS, FragmentMatcher, MACCSkeys, Descriptors, TemplateAlign F./build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/MCS.py:1: DeprecationWarning: The rdkit.Chem.MCS module is deprecated; please use rdkit.Chem.rdFMCS instead. # This work was funded by Roche and generously donated to the free ............[12:51:27] WARNING: More than one matching pattern found - picking one [12:51:27] WARNING: More than one matching pattern found - picking one ........... ====================================================================== FAIL: EnumerateStereoisomers (rdkit.Chem.EnumerateStereoisomers) Doctest: rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/doctest.py", line 2224, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers File "/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/EnumerateStereoisomers.py", line 98, in EnumerateStereoisomers ---------------------------------------------------------------------- File "/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/rdkit/Chem/EnumerateStereoisomers.py", line 210, in rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers Failed example: for smi in sorted(Chem.MolToSmiles(x, isomericSmiles=True) for x in isomers): print(smi) Expected: F[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)Br F[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)Br F[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)Br Got: F[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)Br F[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)Br F[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@H](Cl)[C@@H](Cl)Br ---------------------------------------------------------------------- Ran 25 tests in 333.962s FAILED (failures=1) .. ---------------------------------------------------------------------- Ran 2 tests in 1.182s OK ..s... ---------------------------------------------------------------------- Ran 6 tests in 24.932s OK (skipped=1) .[12:52:11] WARNING: not removing hydrogen atom without neighbors .[12:52:12] WARNING: not removing hydrogen atom without neighbors .[12:52:13] WARNING: no name column found on line 1 [12:52:13] WARNING: no name column found on line 2 [12:52:13] WARNING: no name column found on line 3 [12:52:13] WARNING: no name column found on line 4 [12:52:13] WARNING: no name column found on line 5 [12:52:13] WARNING: no name column found on line 6 [12:52:13] WARNING: no name column 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column found on line 216 ...... ---------------------------------------------------------------------- Ran 9 tests in 3.941s OK .................. ---------------------------------------------------------------------- Ran 18 tests in 22.466s OK ... ---------------------------------------------------------------------- Ran 3 tests in 2.218s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 1.036s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.540s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.468s OK . ---------------------------------------------------------------------- Ran 1 test in 2.843s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.051s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.098s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.060s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.118s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.380s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.483s OK .... ---------------------------------------------------------------------- Ran 4 tests in 94.084s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 1.385s OK . ---------------------------------------------------------------------- Ran 1 test in 0.009s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.123s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 2.593s OK ..................... ---------------------------------------------------------------------- Ran 21 tests in 187.082s OK . ---------------------------------------------------------------------- Ran 1 test in 0.010s OK ...[12:59:17] **** Pre-condition Violation molecule has no conformers Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp Failed Expression: dp_mol->getNumConformers() **** . ---------------------------------------------------------------------- Ran 4 tests in 0.581s OK .. ---------------------------------------------------------------------- Ran 2 tests in 403.808s OK .. ---------------------------------------------------------------------- Ran 2 tests in 3.087s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.325s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.580s OK .....[13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors [13:06:43] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- Ran 10 tests in 9.574s OK ssssss.....s..... ---------------------------------------------------------------------- Ran 17 tests in 3.706s OK (skipped=7) s ---------------------------------------------------------------------- Ran 1 test in 0.001s OK (skipped=1) .......... ---------------------------------------------------------------------- Ran 10 tests in 12.525s OK ..[13:07:32] SMARTS Parse Error: syntax error for input: 'boromicacid' [13:07:32] SMARTS Parse Error: syntax error for input: 'carboxylicacid,acidchlroide' [13:07:32] SMARTS Parse Error: syntax error for input: 'carboxyliccaid,acidchloride' [13:07:32] reaction has no reactants [13:07:32] reaction has no products [13:07:32] initialization failed [13:07:32] reaction has no reactants [13:07:32] reaction has no products . ---------------------------------------------------------------------- Ran 3 tests in 0.720s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.313s OK !!! TEST FAILURE: python UnitTestMCS.py {} !!! TEST FAILURE: python UnitTestMol3D.py {} !!! TEST FAILURE: python UnitTestDocTestsChem.py {} 99% tests passed, 2 tests failed out of 142 Total Test time (real) = 5910.39 sec The following tests FAILED: 28 - graphmoltestPickler (Child aborted) 141 - pythonTestDirChem (Failed) Errors while running CTest make[2]: *** [Makefile:144: test] Error 8 make[2]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' dh_auto_test: cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=-j4 returned exit code 2 make[1]: [debian/rules:106: override_dh_auto_test] Error 2 (ignored) make[1]: Leaving directory '/build/rdkit-201809.1+dfsg' fakeroot debian/rules binary dh binary --with python2 --buildsystem=cmake --parallel dh_testroot -O--buildsystem=cmake -O--parallel dh_prep -O--buildsystem=cmake -O--parallel dh_installdirs -O--buildsystem=cmake -O--parallel dh_auto_install -O--buildsystem=cmake -O--parallel cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/rdkit-201809.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/rdkit-201809.1+dfsg -B/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/External/catch /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/catch /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/External/INCHI-API /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'External/catch/CMakeFiles/catch.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/External/INCHI-API && /usr/bin/cmake -E copy /build/rdkit-201809.1+dfsg/External/INCHI-API/python/noinchi.py /build/rdkit-201809.1+dfsg/rdkit/Chem/inchi.py [ 0%] Built target catch make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/Cluster/Murtagh /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= [ 0%] Built target inchi_support make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 1%] Built target hc [ 3%] Built target RDGeneral make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDBoost /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/RDBoost/CMakeFiles/RDBoost.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/testRDValue.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/RDGeneral/CMakeFiles/testDict.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DataStructs/CMakeFiles/DataStructs.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 3%] Built target RDBoost make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend [ 3%] Built target testRDValue make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend [ 4%] Built target testDict make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/EigenSolvers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Catalogs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= [ 6%] Built target DataStructs make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Query /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Query /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Numerics/CMakeFiles/testMatrices.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Catalogs/CMakeFiles/Catalogs.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Query/CMakeFiles/testQuery.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 6%] Built target testMatrices make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= [ 7%] Built target EigenSolvers [ 7%] Built target Catalogs make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend [ 8%] Built target testQuery make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/SimDivPickers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/Cluster/Murtagh /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 9%] Built target testMatCalc make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build [ 9%] Built target SimDivPickers make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/RDBoost/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 10%] Built target InfoTheory make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= [ 10%] Built target Clustering make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testDataStructs.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 10%] Built target rdBase make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend [ 10%] Built target rdMetricMatrixCalc make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DataStructs/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build [ 11%] Built target testDataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testFPB.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build [ 12%] Built target testFPB make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/SimDivPickers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DataStructs/CMakeFiles/testMultiFPB.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build [ 13%] Built target testMultiFPB make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/SimDivPickers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Geometry/CMakeFiles/RDGeometryLib.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build [ 14%] Built target RDGeometryLib make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend [ 15%] Built target testSimDivPickers make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/InfoTheory/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ML/Data /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 17%] Built target cDataStructs make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build [ 18%] Built target rdSimDivPickers make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 18%] Built target ChemicalFeatures make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ML/Data/CMakeFiles/cQuantize.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Geometry/CMakeFiles/testTransforms.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 18%] Built target cQuantize make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Geometry/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= [ 18%] Built target rdInfoTheory make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend [ 19%] Built target testTransforms make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Geometry/CMakeFiles/testGrid.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build [ 19%] Built target testGrid make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 19%] Built target Alignment make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend [ 20%] Built target rdGeometry make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Alignment/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build [ 20%] Built target testChemicalFeatures make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 20%] Built target testAlignment make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/GraphMol.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Built target GraphMol make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= [ 25%] Built target rdAlignment make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Built target Trajectory make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 25%] Built target SubstructMatch make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= [ 25%] Built target MolTransforms make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend [ 27%] Built target SmilesParse make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 27%] Built target PartialCharges make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend [ 27%] Built target Subgraphs make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= [ 27%] Built target MolInterchange make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend [ 28%] Built target MolCatalog make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ChemicalFeatures/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 29%] Built target SLNParse make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= [ 29%] Built target rdtrajectory make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= [ 30%] Built target rdqueries make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= [ 30%] Built target rdChemicalFeatures make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build [ 31%] Built target Optimizer make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build [ 32%] Built target graphmolqueryTest make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend [ 33%] Built target Depictor make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend [ 33%] Built target graphmolcpTest make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Built target graphmoltestCanon make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/test-valgrind.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 33%] Built target graphmolMemTest1 make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend [ 34%] Built target graphmolIterTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend [ 35%] Built target test-valgrind make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend [ 36%] Built target ChemTransforms make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build [ 36%] Built target smaTest1 make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 37%] Built target smiTest2 make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build [ 38%] Built target FilterCatalog make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 40%] Built target Fingerprints make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= [ 40%] Built target testSubgraphs1 make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend [ 41%] Built target testSubgraphs2 make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/PartialCharges/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 42%] Built target FragCatalog make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= [ 43%] Built target rdPartialCharges make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend [ 43%] Built target testPartialCharges make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= [ 43%] Built target rdMolTransforms make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 44%] Built target MolChemicalFeatures make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend [ 44%] Built target ReducedGraphs make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 45%] Built target ShapeHelpers make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SLNParse/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= [ 46%] Built target SubstructLibrary make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 46%] Built target rdMolInterchange make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/Numerics/Optimizer /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= [ 47%] Built target rdSLNParse make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend [ 48%] Built target testSLNParse make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ForceField /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 48%] Built target testOptimizer make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 50%] Built target rdchem make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ForceField/CMakeFiles/ForceField.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 50%] Built target rdFingerprintGenerator make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend [ 53%] Built target FileParsers make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend [ 57%] Built target ForceField make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 58%] Built target rdMolChemicalFeatures make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 58%] Built target testReducedGraphs make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 58%] Built target substructLibraryTest make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolInterchange /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 58%] Built target rdShapeHelpers make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend [ 58%] Built target rdReducedGraphs make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 58%] Built target rdSubstructLibrary make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 58%] Built target molInterchangeTest1 make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 58%] Built target graphmolMolOpsTest make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend [ 59%] Built target ForceFieldHelpers make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= [ 59%] Built target graphmolTestsCatch make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend [ 61%] Built target rdmolfiles make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/molBundleTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 61%] Built target graphmoltestChirality make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend [ 61%] Built target molBundleTest [ 62%] Built target graphmoltestPickler make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= [ 62%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Depictor/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/hanoiTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Built target hanoiTest make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target resMolSupplierTest make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend [ 63%] Built target testDepictor make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target rdDepictor make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= [ 63%] Built target cxsmilesTest make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend [ 63%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 63%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= [ 63%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend [ 64%] Built target testMolSupplier make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend [ 64%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 64%] Built target testSequence make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Substruct /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 64%] Built target testExtendedStereoParsing make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= [ 65%] Built target fileParsersCatchTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend [ 65%] Built target fileParsersTest1 make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 65%] Built target testSubstructMatch make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 66%] Built target testChemTransforms make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= [ 66%] Built target filterCatalogTest make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FragCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= [ 68%] Built target Descriptors make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 68%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend [ 69%] Built target rdfiltercatalog make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 70%] Built target testFingerprints [ 71%] Built target rdfragcatalog make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target testMolTransforms [ 71%] Built target testFingerprintGenerators make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend [ 71%] Built target testFeatures make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend [ 71%] Built target rdForceFieldHelpers make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target testMolCatalog make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 72%] Built target rdMolCatalog make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/depend [ 73%] Built target MolHash make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Trajectory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target MMPA make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend [ 73%] Built target FMCS make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ForceField/UFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DistGeom /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DistGeom/CMakeFiles/DistGeometry.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 74%] Built target trajectoryTest make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= [ 74%] Built target DistGeometry make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ForceField/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= [ 74%] Built target testUFFForceField make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DistGeom /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= [ 76%] Built target StructChecker make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/DistGeom/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DistGeom/CMakeFiles/testDistGeom.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target testDistGeom make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target MolAlign make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= [ 77%] Built target rdForceField make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 77%] Built target DistGeom make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/CMakeFiles/graphmolTest1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build [ 78%] Built target graphmolTest1 make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Descriptors/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 78%] Built target testDescriptors make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 78%] Built target testAUTOCORR2D make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ShapeHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Built target ChemReactions make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Built target rdMolDescriptors make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Built target testShapeHelpers make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/FMCS/Test /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 81%] Built target testFMCS [ 81%] Built target rdMolAlign make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/depend [ 81%] Built target rdFMCS make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolHash/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build [ 82%] Built target FMCStest make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MMPA/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= [ 83%] Built target rdMolHash make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build.make Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolHash/CMakeFiles/testMolHash.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 83%] Built target testMolHash [ 83%] Built target testMMPA make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/depend make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend [ 84%] Built target rdMMPA make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/StructChecker/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/StructChecker/CMakeFiles/testStructChecker.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= [ 84%] Built target testStructChecker make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build.make Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/StructChecker/Wrap/CMakeFiles/rdStructChecker.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 84%] Built target rdStructChecker make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build [ 84%] Built target RGroupDecomposition make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 85%] Built target DistGeomHelpers make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 86%] Built target testReaction make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend [ 90%] Built target MolStandardize make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ChemReactions/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= [ 91%] Built target testEnumeration make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 91%] Built target testReactionFingerprints make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/UFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 91%] Built target rxnTestCatch make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 91%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 91%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/DistGeomHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= [ 92%] Built target rdChemReactions make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolAlign /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 92%] Built target testCrystalForceField make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build [ 92%] Built target testDistGeomHelpers make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 93%] Built target testMolAlign make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 94%] Built target rdDistGeom make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= [ 94%] Built target testRGroupDecomp make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build [ 94%] Built target MolDraw2D make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 94%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= [ 95%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend [ 95%] Built target molStandardizeTest [ 95%] Built target rdRGroupDecomposition make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 96%] Built target molChargeTest [ 97%] Built target molTautomerTest make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend [ 97%] Built target molFragmentTest make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend [ 97%] Built target molStandardizeSmallTest make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolStandardize/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/ForceField/MMFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [ 97%] Built target moldraw2DRxnTest1 make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend [ 98%] Built target testMMFFForceField [ 99%] Built target moldraw2DTest1 make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' cd /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-201809.1+dfsg /build/rdkit-201809.1+dfsg/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= [100%] Built target rdMolStandardize make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [100%] Built target rdMolDraw2D make[3]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build'. make[3]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' [100%] Built target rdmolops make[2]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/rdkit-201809.1+dfsg/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/_py2_pickle.py -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/RDConfig.py -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/FeatFinderCLI.py -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/SimpleEnum -- Installing: 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/build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/DistanceGeometry/DistGeom.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitCatalogs.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitCatalogs.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitGraphMol.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitGraphMol.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Atom.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Bond.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Canon.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/details.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Rings.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h -- 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/build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdDepictor.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSmilesParse.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/primes.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitFileParsers.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitFileParsers.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSubstructMatch.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitChemReactions.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitChemReactions.so -- Installing: 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/build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitChemTransforms.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSubgraphs.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitSubgraphs.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 -- Installing: 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/build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolDescriptors.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitFingerprints.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitFingerprints.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairs.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/Fingerprints.h -- Installing: 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/build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdFingerprintGenerator.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitPartialCharges.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitPartialCharges.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdPartialCharges.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolTransforms.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolTransforms.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolTransforms.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolTransforms.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/UFF.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdForceFieldHelpers.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdDistGeom.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolAlign.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolAlign.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolAlign.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolChemicalFeatures.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitShapeHelpers.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdShapeHelpers.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolCatalog.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolCatalog.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolCatalog.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DDetails.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolDraw2D.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/rdMolDraw2D.so 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/build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FMCS/SubstructMatchCustom.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/FMCS/MaximumCommonSubgraph.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdFMCS.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolHash.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolHash.so.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMolHash.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolHash.so -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMMPA.so.1.2018.09.1 -- Installing: /build/rdkit-201809.1+dfsg/debian/tmp/usr/lib/libRDKitMMPA.so.1 -- Installing: 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debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/source/rdkit.Chem.PandasTools.rst exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.BitRank.rst exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdStructChecker.rst exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.canvasbase.rst exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/exts/extapi.py exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_7.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_0.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/similarity_map_charges.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_8.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_12.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/cdk2_mol1.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_11.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_10.jpg exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_10.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_2.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/indole1.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_4.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_9.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_1.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/cdk2_mol2.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/similarity_map_rf.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_3.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_5.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/images/picture_6.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example10.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example11.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example3.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example13.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example4.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example1.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example9.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example15.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example8.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example2.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example14.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example12.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example6.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example5.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example7.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/C++Examples/example16.cpp exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/bzr.sdf exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/solubility.test.sdf exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/input.mol exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/bzr.smi exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/cdk2.sdf exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/solubility.train.sdf exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/invalid.mol exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/chiral.mol exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Book/data/AmideBond.rxn exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Images/logo.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Images/logo.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Images/logo.lrg.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Images/logo_plain.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Images/logo.ai exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/EnhancedStereo.md exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/CodingStandards.md exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png 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 (47), librdkit1 (92), postgresql-11-rdkit (0), python-rdkit (1), rdkit-data (3), 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.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built For a short-term work-around: Add the files to debian/not-installed mkdir -p /build/rdkit-201809.1+dfsg/debian/rdkit-doc/usr/share/doc/rdkit/ cp /build/rdkit-201809.1+dfsg/Docs/Book/_build/latex/RDKit.pdf /build/rdkit-201809.1+dfsg/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/rdkit-201809.1+dfsg/Docs/Book/_build/html /build/rdkit-201809.1+dfsg/debian/rdkit-doc/usr/share/doc/rdkit/ pg_buildext install /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit build-%v postgresql-%v-rdkit ### install 11 ### make[2]: Entering directory '/build/rdkit-201809.1+dfsg/build-11' /bin/mkdir -p '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib' /bin/mkdir -p '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/share/postgresql/11/extension' /bin/mkdir -p '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/share/postgresql/11/extension' /usr/bin/install -c -m 755 rdkit.so '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/rdkit.so' /usr/bin/install -c -m 644 /build/rdkit-201809.1+dfsg/Code/PgSQL/rdkit/rdkit.control '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/share/postgresql/11/extension/' /usr/bin/install -c -m 644 rdkit--3.7.sql '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/share/postgresql/11/extension/' /bin/mkdir -p '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode/rdkit' /bin/mkdir -p '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/ /usr/bin/install -c -m 644 rdkit_io.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 mol_op.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_op.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 sfp_op.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rxn_op.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rdkit_gist.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gist.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gin.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 low_gist.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 guc.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 cache.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 adapter.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bitstring.bc '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode'/rdkit/./ cd '/build/rdkit-201809.1+dfsg/debian/postgresql-11-rdkit/usr/lib/postgresql/11/lib/bitcode' && /usr/lib/llvm-7/bin/llvm-lto -thinlto -thinlto-action=thinlink -o rdkit.index.bc rdkit/rdkit_io.bc rdkit/mol_op.bc rdkit/bfp_op.bc rdkit/sfp_op.bc rdkit/rxn_op.bc rdkit/rdkit_gist.bc rdkit/bfp_gist.bc rdkit/bfp_gin.bc rdkit/low_gist.bc rdkit/guc.bc rdkit/cache.bc rdkit/adapter.bc rdkit/bitstring.bc make[2]: Leaving directory '/build/rdkit-201809.1+dfsg/build-11' make[1]: Leaving directory '/build/rdkit-201809.1+dfsg' dh_installdocs -O--buildsystem=cmake -O--parallel debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/rdkit-201809.1+dfsg' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/rdkit-201809.1+dfsg' debian/rules override_dh_python2 make[1]: Entering directory '/build/rdkit-201809.1+dfsg' dh_python2 -ppython-rdkit I: dh_python2 fs:343: renaming rdBase.so to rdBase.arm-linux-gnueabihf.so /usr/share/dh-python/dh_python2:67: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead 'libpython%s: %s', so_version, fn) W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdBase.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdChemReactions.so to rdChemReactions.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdChemReactions.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdChemicalFeatures.so to rdChemicalFeatures.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdChemicalFeatures.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdDepictor.so to rdDepictor.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdDepictor.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdDistGeom.so to rdDistGeom.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdDistGeom.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdFMCS.so to rdFMCS.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdFMCS.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdFingerprintGenerator.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdForceFieldHelpers.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMMPA.so to rdMMPA.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMMPA.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolAlign.so to rdMolAlign.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolAlign.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolCatalog.so to rdMolCatalog.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolCatalog.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolChemicalFeatures.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolDescriptors.so to rdMolDescriptors.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolDescriptors.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolHash.so to rdMolHash.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolHash.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolInterchange.so to rdMolInterchange.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolInterchange.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolTransforms.so to rdMolTransforms.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolTransforms.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdPartialCharges.so to rdPartialCharges.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdPartialCharges.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdRGroupDecomposition.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdReducedGraphs.so to rdReducedGraphs.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdReducedGraphs.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdSLNParse.so to rdSLNParse.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdSLNParse.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdShapeHelpers.so to rdShapeHelpers.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdShapeHelpers.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdStructChecker.so to rdStructChecker.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdStructChecker.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdSubstructLibrary.so to rdSubstructLibrary.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdSubstructLibrary.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdchem.so to rdchem.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdchem.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdfiltercatalog.so to rdfiltercatalog.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdfiltercatalog.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdfragcatalog.so to rdfragcatalog.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdfragcatalog.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdmolfiles.so to rdmolfiles.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdmolfiles.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdmolops.so to rdmolops.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdmolops.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdqueries.so to rdqueries.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdqueries.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdtrajectory.so to rdtrajectory.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdtrajectory.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolDraw2D.so to rdMolDraw2D.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolDraw2D.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMolStandardize.so to rdMolStandardize.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMolStandardize.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming cDataStructs.so to cDataStructs.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: cDataStructs.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdGeometry.so to rdGeometry.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdGeometry.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming DistGeom.so to DistGeom.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: DistGeom.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdAlignment.so to rdAlignment.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdAlignment.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdMetricMatrixCalc.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdSimDivPickers.so to rdSimDivPickers.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdSimDivPickers.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdForceField.so to rdForceField.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdForceField.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming cQuantize.so to cQuantize.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: cQuantize.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming Clustering.so to Clustering.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: Clustering.arm-linux-gnueabihf.so I: dh_python2 fs:343: renaming rdInfoTheory.so to rdInfoTheory.arm-linux-gnueabihf.so W: dh_python2 dh_python2:67: public extension linked with libpython2.7: rdInfoTheory.arm-linux-gnueabihf.so dh_numpy -ppython-rdkit make[1]: Leaving directory '/build/rdkit-201809.1+dfsg' dh_installinit -O--buildsystem=cmake -O--parallel dh_lintian -O--buildsystem=cmake -O--parallel dh_perl -O--buildsystem=cmake -O--parallel dh_link -O--buildsystem=cmake -O--parallel dh_strip_nondeterminism -O--buildsystem=cmake -O--parallel dh_compress -O--buildsystem=cmake -O--parallel dh_fixperms -O--buildsystem=cmake -O--parallel dh_missing -O--buildsystem=cmake -O--parallel dh_strip -O--buildsystem=cmake -O--parallel dh_makeshlibs -O--buildsystem=cmake -O--parallel dh_shlibdeps -O--buildsystem=cmake -O--parallel dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDataStructs.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFragCatalog.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitInfoTheory.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDepictor.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolChemicalFeatures.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitEigenSolvers.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSmilesParse.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolAlign.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitCatalogs.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitAlignment.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRGroupDecomposition.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitPartialCharges.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitReducedGraphs.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFMCS.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDGeometryLib.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitOptimizer.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolDraw2D.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSubstructLibrary.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSubgraphs.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolHash.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitTrajectory.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFileParsers.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSimDivPickers.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitChemReactions.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitGraphMol.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDistGeomHelpers.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDBoost.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolStandardize.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitChemicalFeatures.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolTransforms.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitForceFieldHelpers.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMMPA.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSubstructMatch.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSLNParse.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDistGeometry.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolCatalog.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFingerprints.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFilterCatalog.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolInterchange.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDGeneral.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitForceField.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDescriptors.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitShapeHelpers.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitStructChecker.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitChemTransforms.so.1.2018.09.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/librdkit1/usr/lib/libRDKitMolAlign.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitDistGeomHelpers.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitForceFieldHelpers.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitDistGeometry.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitForceField.so.1.2018.09.1 were not linked against libRDKitOptimizer.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/librdkit1/usr/lib/libRDKitMolAlign.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitOptimizer.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitDistGeomHelpers.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitForceFieldHelpers.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitDistGeometry.so.1.2018.09.1 debian/librdkit1/usr/lib/libRDKitForceField.so.1.2018.09.1 were not linked against libRDKitTrajectory.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolChemicalFeatures.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Numerics/rdAlignment.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdchem.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdDepictor.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolInterchange.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdChemReactions.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/ML/InfoTheory/rdInfoTheory.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdSLNParse.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdmolops.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdReducedGraphs.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolHash.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdRGroupDecomposition.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdfragcatalog.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/rdMolDraw2D.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdPartialCharges.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdFMCS.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/ML/Data/cQuantize.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdSubstructLibrary.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolTransforms.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdqueries.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/DistanceGeometry/DistGeom.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdForceFieldHelpers.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolAlign.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdtrajectory.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/DataStructs/cDataStructs.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdShapeHelpers.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/SimDivFilters/rdSimDivPickers.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/ML/Cluster/Clustering.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/rdBase.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Geometry/rdGeometry.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/MolStandardize/rdMolStandardize.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/ForceField/rdForceField.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdChemicalFeatures.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdFingerprintGenerator.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdfiltercatalog.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolCatalog.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdDistGeom.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdmolfiles.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolDescriptors.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMMPA.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdStructChecker.arm-linux-gnueabihf.so were not linked against libboost_serialization.so.1.67.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdChemReactions.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdmolops.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolHash.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/rdMolDraw2D.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolTransforms.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/DistanceGeometry/DistGeom.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolAlign.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdShapeHelpers.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/MolStandardize/rdMolStandardize.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdDistGeom.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolDescriptors.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdStructChecker.arm-linux-gnueabihf.so were not linked against libRDKitEigenSolvers.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/DistanceGeometry/DistGeom.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdForceFieldHelpers.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolAlign.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/ForceField/rdForceField.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdDistGeom.arm-linux-gnueabihf.so were not linked against libRDKitOptimizer.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolChemicalFeatures.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdchem.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdDepictor.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolInterchange.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdChemReactions.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdSLNParse.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdmolops.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdReducedGraphs.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolHash.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdRGroupDecomposition.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdfragcatalog.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/rdMolDraw2D.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdPartialCharges.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdFMCS.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdSubstructLibrary.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolTransforms.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdqueries.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/DistanceGeometry/DistGeom.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdForceFieldHelpers.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolAlign.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdtrajectory.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdShapeHelpers.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/MolStandardize/rdMolStandardize.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/ForceField/rdForceField.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdChemicalFeatures.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdFingerprintGenerator.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdfiltercatalog.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolCatalog.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdDistGeom.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdmolfiles.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMolDescriptors.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdMMPA.arm-linux-gnueabihf.so debian/python-rdkit/usr/lib/python2.7/dist-packages/rdkit/Chem/rdStructChecker.arm-linux-gnueabihf.so were not linked against libcoordgenlibs.so.1 (they use none of the library's symbols) dh_installdeb -O--buildsystem=cmake -O--parallel dh_gencontrol -O--buildsystem=cmake -O--parallel dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-11-rdkit: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-11-rdkit: substitution variable ${python: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 rdkit-doc: substitution variable ${python:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake -O--parallel dh_builddeb -O--buildsystem=cmake -O--parallel dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_201809.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_201809.1+dfsg-6_all.deb'. dpkg-deb: building package 'python-rdkit' in '../python-rdkit_201809.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'postgresql-11-rdkit' in '../postgresql-11-rdkit_201809.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'postgresql-11-rdkit-dbgsym' in '../postgresql-11-rdkit-dbgsym_201809.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'librdkit1' in '../librdkit1_201809.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'python-rdkit-dbgsym' in '../python-rdkit-dbgsym_201809.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'librdkit1-dbgsym' in '../librdkit1-dbgsym_201809.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_201809.1+dfsg-6_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rdkit_201809.1+dfsg-6_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/9958/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/9958/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/9958 and its subdirectories I: Current time: Sat Jul 11 13:54:02 +14 2020 I: pbuilder-time-stamp: 1594425243